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[
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-j",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a pyrimidine sequence avoiding PPT pairing.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, pyrimidine sequence avoiding PPT pairing.",
        "title": "Exonic splicing for pyrimidine sequence",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-j-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-i",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 72h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 72h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-i-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-b",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Geldanamycin",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-b-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000088-b",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A deep mutational scan of influenza nucleoprotein was performed to measure the fitness landscape, e.g. enumerate the mutants likely to produce viable viruses. Two homologs of nucleoprotein were scanned: one from H1N1 PR/1934 and one from H3N2 Aichi/1968. Because effects of single mutants in two highly similar (94% identical) sequence contexts were measured, small contrasts can be drawn between the score sets.",
        "method_text": "Mutants were introduced by NNN PCR into nucleoprotein from influenza H3N2 Aichi/1968. Co-cultures of 293T and MDCK-SIAT1 cells were co-transfected with the nucleoprotein mutant library, and the remaining 7 influenza genes (PB1/PB2/PA from Nanchang/933/1995 and HA/NA/M/NS from WSN/1933). Together these make for a complete virion, which can replicate when the mutant nucleoprotein is functional.\r\n\r\nViruses were then passaged in MDCK-SIAT1 cells at low multiplicity of infection (MOI). Viruses were then collected from cells, RNA was extracted and reverse-transcribed, followed by DNA sequencing. Sequencing quantified which nucleoprotein variants were more versus less abundant in the population of passaged (replicated) viruses, a measure of the fitness of the variant for successful virus replication.",
        "short_description": "Deep mutational scan of H3N2 Aichi/1968 nucleoprotein assaying for viral replication.",
        "title": "Influenza H3N2 Aichi/1968 nucleoprotein",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP056028",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP056028",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "26226986",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26226986",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000088-b-1"
        ],
        "experimentset": "urn:mavedb:00000088"
    },
    {
        "creation_date": "2021-11-02",
        "modification_date": "2021-11-02",
        "urn": "urn:mavedb:00000085-d",
        "publish_date": "2021-11-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 β-lactamase gene in *Escherichia coli* on different backgrounds. Fitness measurements were estimated based on growth under increasing concentrations of cefotaxime using a band-pass selection system.",
        "method_text": "The variant library was constructed using PFunkel comprehensive codon mutagenesis. One NNN-containing mutagenic primer was used per codon.\r\n\r\nThis dataset describes variants on the TEM-15 background, which differs from TEM-1 by p.[Glu102Lys;Gly236Ser] (TEM-1 position not Ambler position).\r\n\r\nThe band-pass selection system is described in (Sohka et al., 2009). Briefly, cells are plated on media containing Tet and a variable concentration of cefotaxime. If TEM-1 activity is too low for the cefotaxime concentration, cells will not proliferate. If TEM-1 activity is too high, no cell wall damage will occur and TetC (which confers Tet resistance) will not be produced. Therefore cells should only grow if the TEM-1 variant’s activity level matches the cefotaxime concentration.\r\n\r\nSequencing was performed using PacBio.",
        "short_description": "TEM-15 (TEM-1 variant) fitness on cefotaxime.",
        "title": "TEM-15 cefotaxime",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "27173379",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27173379",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000085-d-1"
        ],
        "experimentset": "urn:mavedb:00000085"
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-b",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 16 µg/mL ampicillin at 25C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 16 µg/mL ampicillin at 25C",
        "title": "VIM-2 16 µg/mL AMP at 25C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-b-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-c",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an SRSF7 (9G8) binding site.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an SRSF7 (9G8) binding site.",
        "title": "Exonic splicing for SRSF7 (9G8) binding site",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-c-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2019-02-18",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000013-b",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study demonstrated variant abundance by massively parallel sequencing (VAMP-seq), a technique for measuring the effect of protein variants on abundance using fluorescence. VAMP-seq is a generally-applicable assay for protein stability that can identify loss-of-function variants.",
        "method_text": "Barcoded variant libraries were created using inverse PCR. Barcodes were associated with full-length variants using Pacific Biosciences SMRT sequencing to generate long reads. Each protein variant is fused to EGFP so that its abundance can be tracked using fluorescence. Cells were sorted into bins using FACS based on the ratio of EGFP to mCherry.",
        "short_description": "Variant abundance by massively parallel sequencing (VAMP-seq) applied to TPMT.",
        "title": "TMPT VAMP-seq",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "SMRT sequencing"
            },
            {
                "text": "FACS"
            },
            {
                "text": "VAMP-seq"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA428380",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA428380",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000013-b-1"
        ],
        "experimentset": "urn:mavedb:00000013"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000027-b",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of PKLR promoter, 48h post-transfection in K562 cells.",
        "title": "Saturation mutagenesis MPRA of PKLR promoter, 48h",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "PKLR"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444728",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444728",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000027-b-1"
        ],
        "experimentset": "urn:mavedb:00000027"
    },
    {
        "creation_date": "2020-08-07",
        "modification_date": "2021-01-18",
        "urn": "urn:mavedb:00000059-a",
        "publish_date": "2021-01-18",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "To comprehensively characterize the consequences of the p53 mutation spectrum, the author generated ~10,000 variants on the DNA-binding domain (DBD) of p53 variants in human cells and measured the relative growth rate of each mutant through selection.",
        "method_text": "The designed variant library of p53 are separated to 4 groups and synthesized using Agilent microarrays which contains a contiguous mutated region. The sequences are transformed into a lentiviral vector. The packaged virus then infected p53-null H1299 cells. The cells were incubated for 14 days and the variant frequency change for the cells are determined on day 2, 6, 9 and 14 using next-generation sequencing.\r\nMissense mutations are grouped according to the position of substitution: 1-48 in sub-library DBDA, 49-96 in sub-library DBDB, 97-144 in sub-library DBDC and the rest are in DBDD.",
        "short_description": "The impact of p53 variant is represented by the frequency change of cells harboring that mutation over several time point.",
        "title": "p53 variant effect measured by cell growth",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29979965",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29979965",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000059-a-1"
        ],
        "experimentset": "urn:mavedb:00000059"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-d",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the presence of the antibiotic to perform the selection. Two replicate selections were performed.\r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 625 μg/ml",
        "title": "TEM-1 625 μg/ml Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-d-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2019-01-24",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000008-a",
        "publish_date": "2019-01-24",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study described the functional consequence of over 100,000 enhancer variants *in vivo* in mouse liver. Two human enhancers (ALDOB, ECR11) and one mouse enhancer (LTV1) were known to be active in mouse liver and therefore variants in these enhancers should show a measurable difference in transcription. The results were broadly consistent with evolutionary data and transcription factor binding sites, but were not always concordant demonstrating the importance of measuring the effect of enhancer variants directly.\r\n\r\nThis MaveDB entry describes the LTV1 enhancer data. Datasets for other enhancers described in the same publication are also available: [ALDOB](https://www.mavedb.org/experiment/urn:mavedb:00000006-a/) [ECR11](https://www.mavedb.org/experiment/urn:mavedb:00000007-a/)",
        "method_text": "Variants were constructed using doped oligo with 1% of each non-target base included at each position (ratio of 97:1:1:1). Full-length enhancer haplotypes were assembled and cloned into tagged pGL4.23 plasmids. Each variant haplotype was tagged with a 20-bp sequence, with multiple tags per haplotype in each replicate in most cases. Each single nucleotide change was present in at least 42 haplotypes. \r\n\r\nThe enhancers were injected into the mouse tail vein and mouse livers were harvested after 24h. RNA was isolated from fresh mouse livers, subjected to DNAseI treatment to remove any DNA contamination, reverse-transcribed into cDNA, and sequenced.\r\n\r\nTwo sets of sequencing reactions were performed. One used short Illumina reads (42 total cycles) to sequence the tag sequence used for quantifying each enhancer's activity. The other used subassembly synthetic long read sequencing to associate the tags with the full-length enhancer haplotypes.",
        "short_description": "Massively parallel functional dissection of the LTV1 enhancer in a mouse liver transcription assay.",
        "title": "Massively parallel functional dissection of LTV1 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "liver"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRA049159",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRA049159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22371081",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22371081",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000008-a-1",
            "urn:mavedb:00000008-a-2"
        ],
        "experimentset": "urn:mavedb:00000008"
    },
    {
        "creation_date": "2021-03-14",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000063-a",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of <i>E.coli</i> dihydrofolate reductase (DHFR) whose function is necessary for the survival of the bacteria. The study cultured the bacteria in an early Log phase growth period under the control of Lon protease and determined the variant frequency change after cultivation, indicating the impact of DHFR variants.",
        "method_text": "The variant library in this study is generated by parallel inverse PCR reactions. An <i>E.coli</i> strain with functioning Lon gene is introduced with the variant library and cultivated. The growth rates of the bacteria harbouring each variant at several timepoints are determined by Illumina NextSeq, and the results are analyzed by Enrich2. The experiments are repeated three times in total and the final fitness values are the average of them.",
        "short_description": "Growth rate of E.coli with mutated dihydrofolate reductase (DHFR) with functioning Lon protease",
        "title": "Growth rate of mutated DHFR with functioning Lon",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA590072",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA590072",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.53476",
                "url": "https://doi.org/10.7554/eLife.53476",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32701056",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32701056",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000063-a-1"
        ],
        "experimentset": "urn:mavedb:00000063"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-s",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 20, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 20 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 20 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-s-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-01-17",
        "urn": "urn:mavedb:00000057-c",
        "publish_date": "2021-01-17",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors used saturation mutagenesis to study the variant effect of Ras, with the regulation of GTPase activating protein (GAP) and guanine nucleotide exchange factor (GEF). The variants were selected by bacterial two-hybrid strategy.",
        "method_text": "The RAS mutant library was generated by oligonucleotide-directed mutagenesis. The mutant library was transfected into bacteria with the regulation of GAP as well as GEF. The functioning RAS protein which will bind to GTP as well as Raf. The binding of these molecules can trigger the transcription of an antibiotic resistant factor. The library was separated to three sub-libraries in order to cover the whole RAS gene length which ranges from the residue 2-56, 57-111, and 112-166. These samples were selected individually. The samples in different sub-libraries were barcoded and pooled together for MiSeq sequencing.",
        "short_description": "In the presence of a GAP and a GEF, selection result on the mutated H-Ras.",
        "title": "Regulated-Ras",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28686159",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28686159",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000057-c-1"
        ],
        "experimentset": "urn:mavedb:00000057"
    },
    {
        "creation_date": "2021-08-16",
        "modification_date": "2021-08-16",
        "urn": "urn:mavedb:00000065-a",
        "publish_date": "2021-08-16",
        "created_by": "0000-0001-6465-5776",
        "modified_by": "0000-0001-6465-5776",
        "extra_metadata": {},
        "abstract_text": "NCS1 variant effect map (Abstract - to be updated)",
        "method_text": "NCS1 variant effect map (Methd - to be updated)",
        "short_description": "NCS1 variant effect map (Short description - to be updated)",
        "title": "NCS1 variant effect map",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6465-5776"
        ],
        "scoresets": [
            "urn:mavedb:00000065-a-1"
        ],
        "experimentset": "urn:mavedb:00000065"
    },
    {
        "creation_date": "2019-02-18",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000013-a",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study demonstrated variant abundance by massively parallel sequencing (VAMP-seq), a technique for measuring the effect of protein variants on abundance using fluorescence. VAMP-seq is a generally-applicable assay for protein stability that can identify loss-of-function variants.",
        "method_text": "Barcoded variant libraries were created using inverse PCR. Barcodes were associated with full-length variants using Pacific Biosciences SMRT sequencing to generate long reads. Each protein variant is fused to EGFP so that its abundance can be tracked using fluorescence. Cells were sorted into bins using FACS based on the ratio of EGFP to mCherry.",
        "short_description": "Variant abundance by massively parallel sequencing (VAMP-seq) applied to PTEN.",
        "title": "PTEN VAMP-seq",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "SMRT sequencing"
            },
            {
                "text": "FACS"
            },
            {
                "text": "VAMP-seq"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA428380",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA428380",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000013-a-1"
        ],
        "experimentset": "urn:mavedb:00000013"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-b",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an SRSF1 (ASF/SF2) binding site.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an SRSF1 (ASF/SF2) binding site.",
        "title": "Exonic splicing for SRSF1 (ASF/SF2) binding site",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-b-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000055-0",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "Meta-analysis of urn:mavedb:00000055-a-1, urn:mavedb:00000055-b-1",
        "title": "Meta-analysis of urn:mavedb:00000055-a-1, urn:mavedb:00000055-b-1",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [],
        "scoresets": [
            "urn:mavedb:00000055-0-1"
        ],
        "experimentset": "urn:mavedb:00000055"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-g",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an hnRNP L binding site.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an hnRNP L binding site.",
        "title": "Exonic splicing for hnRNP L binding site",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-g-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-g",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 5, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 5 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 5 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-g-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-a",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 2h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 2h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-a-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000029-b",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of SORT1 enhancer (reversed orientation) in HepG2 cells.",
        "title": "Saturation mutagenesis MPRA of SORT1 enhancer, flipped",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "SORT1"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444731",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444731",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000029-b-1"
        ],
        "experimentset": "urn:mavedb:00000029"
    },
    {
        "creation_date": "2021-09-24",
        "modification_date": "2021-09-25",
        "urn": "urn:mavedb:00000072-a",
        "publish_date": "2021-09-25",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A deep mutational scan of the CH3 domain of human IgG1 was performed to measure the effect of mutants on stability. Stability selected for by a proxy, binding to either CD64 or an antibody against human CH2 domain. This was performed at 79C under the premise that less stable mutants would be denatured at that temperature and therefore unable to bind.",
        "method_text": "Mutants were introduced into the human Fc by error-prone PCR. The mutant libraries were transformed into Yeast for surface display. Cells were grown and then incubated at 79C in order to denature mutants with reduced stability. Cells were then cooled down and mixed with CD64 and anti-human CH2 antibody fluorescently labeled with FITC. Cells bound with fluorescent molecules were selected by FACS. Selected cells were then sequenced. Enrichment of a mutant post-selection is scored and interpreted as a proxy for stability.",
        "short_description": "Deep mutational scan of human IgG1 (CH3 domain) binding by CD64 and anti-human CH2, under 79C heat stress as a proxy for stability.",
        "title": "Human IgG1 Fc stability",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22846908",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22846908",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-8037-6045"
        ],
        "scoresets": [
            "urn:mavedb:00000072-a-1"
        ],
        "experimentset": "urn:mavedb:00000072"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-h",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 5, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 5 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 5 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-h-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000030-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of TCF7L2 enhancer in MIN6 cells.",
        "title": "Saturation mutagenesis MPRA of TCF7L2 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "TCF7L2"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444733",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444733",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000030-a-1"
        ],
        "experimentset": "urn:mavedb:00000030"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-a",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence present at wild-type Wilms’ tumor gene 1 exon 5.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, Wilms’ tumor gene 1 exon 5.",
        "title": "Exonic splicing for Wilms’ tumor gene",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-a-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-d",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "Degenerate primers and recombination-based cloning were used to create a mutant library of the Fis1p TA protein in a Gal4-sfGFP-Fis1p plasmid. Cells with wild-type-like TA variants would fail to grow, since the Gal4 is localized to the mitochondrial membrane instead of in the nucleus to drive transcription on selective media. Sequencing was performed using a MiSeq Nano (2x150v2).\r\n\r\nThis experiment compares the population grown on supplemented minimal medium (SMM) -Trp -His medium to the baseline population grown on synthetic complete (SC) -Trp.",
        "short_description": "Deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium.",
        "title": "Fis1 tail anchor, SMM -Trp -His",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000076-d-1"
        ],
        "experimentset": "urn:mavedb:00000076"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-e",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "Degenerate primers and recombination-based cloning were used to create a mutant library of the Fis1p TA protein in a Gal4-sfGFP-Fis1p plasmid. Cells with wild-type-like TA variants would fail to grow, since the Gal4 is localized to the mitochondrial membrane instead of in the nucleus to drive transcription on selective media. Sequencing was performed using a MiSeq Nano (2x150v2).\r\n\r\nThis experiment compares the population grown on synthetic complete (SC) -Ura medium to the baseline population grown on SC -Trp.",
        "short_description": "Deep mutational scan of the yeast Fis1 tail anchor, SC -Ura medium.",
        "title": "Fis1 tail anchor, SC -Ura",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000076-e-1"
        ],
        "experimentset": "urn:mavedb:00000076"
    },
    {
        "creation_date": "2019-09-26",
        "modification_date": "2020-04-22",
        "urn": "urn:mavedb:00000043-a",
        "publish_date": "2019-10-08",
        "created_by": "0000-0001-7684-5841",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The single transmembrane domain of the human thrombopoietin receptor (TpoR/MPL), encoded by exon 10 of the MPL gene, is a hotspot for somatic mutations associated with myeloproliferative neoplasms. One experiment was designed to identify all single-amino-acid substitutions in the human TpoR transmembrane and partial juxtamembrane regions (488-516) that could independently confer factor-free growth. A second experiment was designed to determine mutations that enhance the constitutive activity of the patient-derived S505N mutation.",
        "method_text": "The DMS library was encoded in the retroviral expression system pMX-GW-PGK-PuroR-GFP. Each codon for amino acid positions 488-516 of the human TpoR protein, encompassing the TM and partial JM regions, was independently randomised using degenerate (NNN) primers (IDT) to encode all 64 possible codons. Plasmid preparations for all positions (488-516) were pooled together in equal amounts to obtain a library containing all 1,856 possible DNA variants. The frequencies of variants in each library were determined by Illumina sequencing, which confirmed 100% representation across the randomised region and constitutes the unselected control sample.\r\n\r\nThe library was transfected into HEK293T cells along with retroviral packaging vectors using calcium phosphate transfection. After 48 hrs, supernatants containing virus were harvested and sterile filtered for transduction into Ba/F3 cells.  The pooled retroviral library was used to transduce 10^6 Ba/F3 cells at a multiplicity of infection ~0.1, generating ~10^5 transductants for each of six biological replicates. These six cultures were treated with 5 μg/ml puromycin (on IL-3) for 48 hours to yield pure virus-positive cells. Cells for each replicate were split in half and cultured in the continued presence of IL-3, or were washed to remove IL-3, and subjected to another 48 hours culture. mRNA was prepared from the live cells that remained at the end of this procedure.\r\n\r\ncDNA was prepared from 1 μg of total RNA using the TpoR-specific reverse transcription primer containing a 16 bp unique molecular identifier (UMI) and an Illumina adapter. cDNA was amplified to add illumina adapters and indexes for sequencing using an Illumina NextSeq kit with 140 cycles in the forward direction and 160 cycles in the reverse direction.\r\n\r\nThe paired-end reads from Illumina sequencing runs were separated into samples based on Illumina index sequences using Cutadapt v1.157. De-duplication based on the UMI was performed using UMI Tools v1.15 after sample separation. Reads were trimmed to the region of interest and filtered for length using Cutadapt prior to analysis with Enrich2 v1.2.0. \r\n\r\nTo determine mutations that confer constitutive activity log ratio enrichment scores were calculated for each of the six replicates by comparing the variant counts in the unselected plasmid library with those remaining in Ba/F3 cells after 2 days of culture in growth factor free media using “wild-type” (all synonymous DNA sequences encoding the WT amino acid sequence) count normalisation. To determine mutations that confer increased activity on the S505N background six replicates of library-containing BaF3 cells grown in IL-3 were compared to six replicates of library-containing BaF3 cells grown without growth factors.  Log ratios were calculated similarly.",
        "short_description": "Evaluation of all possible single-amino-acid substitutions in the human Thrombopoietin Receptor (Mpl) transmembrane domain for their ability to confer cytokine-independent growth or enhance S505N constitutive activity in Ba/F3 cells.",
        "title": "Novel Drivers and Modifiers of MPL-dependent Oncogenic Transformation Identified by Deep Mutational Scanning",
        "keywords": [
            {
                "text": "Thrombopoietin Receptor"
            },
            {
                "text": "Transmembrane"
            },
            {
                "text": "Enrich2"
            },
            {
                "text": "mRNA"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRR10193506",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRR10193506",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31697803",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31697803",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-7684-5841"
        ],
        "scoresets": [
            "urn:mavedb:00000043-a-1",
            "urn:mavedb:00000043-a-2"
        ],
        "experimentset": "urn:mavedb:00000043"
    },
    {
        "creation_date": "2021-11-11",
        "modification_date": "2021-11-11",
        "urn": "urn:mavedb:00000087-a",
        "publish_date": "2021-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scan of Influenza Nucleoprotein, selecting for viral replication in human MDCK-SIAT1-CMV-PB1 cells.",
        "method_text": "A deep mutational scan of Influenza H3N2 Aichi/1968 Nucleoprotein was performed to characterize the mutation propensity of the virus and inform a phylogenetic tree for Influenza A.  Mutants were introduced using NNN PCR for wildtype H3N2 Aichi/1968 sequence, and for a sequence with the additional variant N334H. Libraries were then selected for viral replication in human MDCK-SIAT1-CMV-PB1 cells across serial dilutions. Variants were sequenced using Illumina.",
        "short_description": "Deep mutational scan of Influenza A (H3N2 Aichi/1968) Nucleoprotein for viral replication.",
        "title": "Influenza A nucleoprotein",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP036064",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP036064",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24859245",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24859245",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-8037-6045"
        ],
        "scoresets": [
            "urn:mavedb:00000087-a-1"
        ],
        "experimentset": "urn:mavedb:00000087"
    },
    {
        "creation_date": "2022-08-16",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000099-a",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study presents a cell-based assay for functional characterization of variants of unknown significance (VUS) in rhodopsin (RHO). 210 previously-observed RHO variants were assayed for cell surface expression using a flow cytometry-based assay.",
        "method_text": "The variant library was constructed from 189 variants from literature, 11 variants from synonymous controls, and 10 additional variants of uncertain significance. Site-directed mutagenesis was used to construct an expression plasmid library containing RHO variants. Each variant plasmid was transfected into HEK293T cells pooled. Two flow cytometry methods were used to compare the 210 variants: standard unpooled flow cytometry assay and a pooled assay.\r\n\r\nThe cells were stained with a fluorescent antibody and were sorted by levels of expression. Immunofluorescence staining distinguishes wildtype RHO from LoF-mutant RHO. Each variant was transfected and sorted into two pools: “high” surface-RHO-expressing cells and “low” surface-RHO-expressing cells.\r\n\r\nTo quantify the pathogenicity of each variant, The residual plasmid was isolated from each cell pool, amplified by PCR and sequenced by Illumina MiSeq.",
        "short_description": "Rhodopsin VUS surface expression",
        "title": "Rhodopsin surface expression",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30977563",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30977563",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000099-a-1"
        ],
        "experimentset": "urn:mavedb:00000099"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-e",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Menadione",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-e-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2021-01-18",
        "urn": "urn:mavedb:00000058-a",
        "publish_date": "2021-01-18",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the molecular determinants of A$\\beta$ 42 aggregation in a cell-based system, by combining a yeast DHFR aggregation assay with deep mutational scanning. The effect of 791 of the 798 possible single amino acid substitutions on the aggregation propensity of A$\\beta$ 42 was measured using a yeast growth-based aggregation assay.",
        "method_text": "The variant library was cloned using in vivo assembly. To measure A$\\beta$ aggregation by yeast growth rate, A$\\beta$ was fused to dihydrofolate reductase (DHFR) via a short peptide linker. DHFR is required for growth and the activity of the fusion protein depends on the solubility of A$\\beta$. When treated with DHFR inhibitor methotrexate, yeast with soluble A$\\beta$ variants grow more rapidly that those with aggregating A$\\beta$ variants. High-throughput DNA sequencing was used to measure the frequency of each variant. Six time points (including the starting time point) were measured during the course of the assay. Three replicate assays were performed.",
        "short_description": "Molecular determinants of Aβ aggregation with Deep Mutational Scanning",
        "title": "Variants of Aβ42 affecting aggregation",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA578530",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA578530",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31558564",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31558564",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000058-a-1"
        ],
        "experimentset": "urn:mavedb:00000058"
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000048-c",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CXCR4 and to map ligand interaction sites. Cells were selected for binding to Ab 12G5.",
        "method_text": "The human CXCR4 sequence was generated by oligo assembly and fused to a c-myc tag. SSM libraries were generated by overlapping PCR using primers with an NNK codon, as described by Procko et al, 2013.\r\nThe SSM library was transfected into CXCR4-knockout human Expi293F cells using pCEP4. \r\nSurface receptor expression was measured by anti-myc-FITC staining and cells were sorted on a BD FACSAria II.\r\nTo test the validity of deep mutational scanning for mapping GPCR interactions sites, cells were selected for binding to fluorescent Ab 12G5, a previously mapped (by small-scale alanine mutagenesis) interacting ligand. \r\nTotal RNA was extracted and PCR-amplified before sequencing by Illumina MiSeq v 3 or HiSeq 2500. \r\n\r\nRaw data available from GEO under accession [GSE100368](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100368).",
        "short_description": "Deep mutational scan selecting for CXCR4 binding to Ab 12G5 in Expi293F cells.",
        "title": "CXCR4 Ab 12G5 binding",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "scoresets": [
            "urn:mavedb:00000048-c-1"
        ],
        "experimentset": "urn:mavedb:00000048"
    },
    {
        "creation_date": "2022-07-28",
        "modification_date": "2022-07-28",
        "urn": "urn:mavedb:00000098-a",
        "publish_date": "2022-07-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scan of 12 amino acids in voltage-sensing helix 4 of human SCN5A, screened for functional protein by challenging HEK293T cells with drug mixture of veratridine+brevetoxin+ouabain.",
        "method_text": "Comprehensive mutagenesis of the 12-amino-acid region (1621-1632aa) of the voltage-sensing helix 4 of human SCN5A, using inverse polymerase chain reaction with degenerate primers. Inserted 18-mer random barcodes into the plasmids, resulting in 7205 unique barcoded plasmids.\r\n\r\nMutants were screened transformed into HEK293T cells and selected for functional protein by challenging cells with a drug mixture of veratridine+brevetoxin+ouabain. The relative function under drugs of 253 mutations were measured. Six replicates were performed.",
        "short_description": "Deep mutational scan of human SCN5A by measuring response to veratridine+brevetoxin+ouabain drugs.",
        "title": "SCN5A response to veratridine+brevetoxin+ouabain mixture",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31928070",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31928070",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-8037-6045"
        ],
        "scoresets": [
            "urn:mavedb:00000098-a-1"
        ],
        "experimentset": "urn:mavedb:00000098"
    },
    {
        "creation_date": "2019-08-08",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000041-a",
        "publish_date": "2019-08-08",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study infers the activity of variants in Src kinases's catalytic domain by measuring their effects on yeast growth, and therefore phosphotransferase activity. The resulting dataset includes variants classified as gain of function, loss of function. or neutral.",
        "method_text": "Variants in the Src catalytic domain were generated using NNK mutagenesis. Barcodes were associated with each variant and barcode-variant mapping was determined using subassembly. Variants were transformed into yeast on plasmids and the plasmid barcodes were sequenced at three time points determined by OD. Barcodes were sequenced on an Illumina NextSeq.",
        "short_description": "Deep mutational scan of the Src kinase catalytic domain.",
        "title": "Deep mutational scan of Src CD",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "kinase"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "NNK mutagenesis"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA464305",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA464305",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30956043",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30956043",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000041-a-1"
        ],
        "experimentset": "urn:mavedb:00000041"
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000047-b",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CCR5 and to map ligand interaction sites. Cells were selected for binding to Ab 2D7.",
        "method_text": "The CCR5 variant library was generated by overlapping PCR using primers with an NNK codon, as described by Procko et al, 2013 and transfected into human Expi293F cells (a cell line lacking CCR5) using pCEP4.\r\nTo test the validity of deep mutational scanning for mapping GPCR interactions sites, cells were selected for binding to fluorescent Ab 2D7, a previously mapped (by small-scale mutagenesis) interacting ligand. \r\nSurface expression was measured using anti-myc-FITC.\r\nCell sorting was performed using a BD FACSAria II.\r\nTotal RNA was extracted and PCR-amplified before sequencing by Illumina MiSeq v3 or HiSeq 2500. \r\nTwo replicate selections were performed.\r\n\r\nRaw data available from GEO under accession [GSE100368](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100368).",
        "short_description": "Deep mutational scan selecting for CCR5 binding to Ab 2D7 in Expi293F cells.",
        "title": "CCR5 Ab 2D7 binding",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "scoresets": [
            "urn:mavedb:00000047-b-1"
        ],
        "experimentset": "urn:mavedb:00000047"
    },
    {
        "creation_date": "2021-07-07",
        "modification_date": "2022-06-08",
        "urn": "urn:mavedb:00000095-b",
        "publish_date": "2022-06-08",
        "created_by": "0000-0002-0730-2576",
        "modified_by": "0000-0002-0730-2576",
        "extra_metadata": {},
        "abstract_text": "This study measured the functional consequences of mutations in CYP2C9, as measured by two different assays, one using Variant Abundance by Massively Parallel sequencing (VAMP-seq) in HEK293T cells, and one using a yeast activity-based protein profiling assay (Click-seq).\r\n\r\nThis entry contains amino acid scores from the abundance assay using VAMP-seq in HEK293T cells.",
        "method_text": "CYP2C9 variant libraries were generated using inverse PCR with NNK primers. Variants were tagged with 18bp random sequence barcodes and the association between barcodes and variants was determined using PacBio sequencing. The barcoded abundance library was introduced into a HEK293T landing pad cell line.\r\n\r\nCells expressing CYP2C9 variants fused to EGFP were sorted into 4 bins by FACS. Genomic DNA was extracted and barcodes from each bin were sequenced. Three replicate sorts were performed. Barcodes from each bin were counted and associated with variant sequences using Enrich2. Variant abundance scores were calculated from the weighed average of variant frequencies in each bin, such that high abundance variants have a higher score and low abundance variants have a lower score. Abundance scores were normalized to the median synonymous variant score (set to 1) and the median nonsense variant score (set to 0). Confidence intervals and variance estimates are based on replicate scores.",
        "short_description": "CYP2C9 protein abundance measured by Variant Abundance by Massively Parallel sequencing (VAMP-seq).",
        "title": "CYP2C9 abundance scores",
        "keywords": [
            {
                "text": "NNK mutagenesis"
            },
            {
                "text": "FACS"
            },
            {
                "text": "VAMP-seq"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE165412",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165412",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "34314704",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/34314704",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-0730-2576"
        ],
        "scoresets": [
            "urn:mavedb:00000095-b-1"
        ],
        "experimentset": "urn:mavedb:00000095"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000088-a",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A deep mutational scan of influenza nucleoprotein was performed to measure the fitness landscape, e.g. enumerate the mutants likely to produce viable viruses. Two homologs of nucleoprotein were scanned: one from H1N1 PR/1934 and one from H3N2 Aichi/1968. Because effects of single mutants in two highly similar (94% identical) sequence contexts were measured, small contrasts can be drawn between the score sets.",
        "method_text": "Mutants were introduced by NNN PCR into nucleoprotein from influenza H1N1 PR/1934. Co-cultures of 293T and MDCK-SIAT1 cells were co-transfected with the nucleoprotein mutant library, and the remaining 7 influenza genes (PB1/PB2/PA from Nanchang/933/1995 and HA/NA/M/NS from WSN/1933). Together these make for a complete virion, which can replicate when the mutant nucleoprotein is functional. \r\n\r\nViruses were then passaged in MDCK-SIAT1 cells at low multiplicity of infection (MOI). Viruses were then collected from cells, RNA was extracted and reverse-transcribed, followed by DNA sequencing. Sequencing quantified which nucleoprotein variants were more versus less abundant in the population of passaged (replicated) viruses, a measure of the fitness of the variant for successful virus replication.",
        "short_description": "Deep mutational scan of H1N1 PR/1934 nucleoprotein assaying for viral replication.",
        "title": "Influenza H1N1 PR/1934 nucleoprotein",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP056028",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP056028",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "26226986",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26226986",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000088-a-1"
        ],
        "experimentset": "urn:mavedb:00000088"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-v",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 21, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 21 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 21 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-v-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-01-28",
        "modification_date": "2021-01-29",
        "urn": "urn:mavedb:00000060-a",
        "publish_date": "2021-01-29",
        "created_by": "0000-0002-9712-9163",
        "modified_by": "0000-0002-9712-9163",
        "extra_metadata": {},
        "abstract_text": "Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause cellular toxicity is still not clear, even in simpler cellular systems. We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity. We generated >50,000 mutations in the prion-like domain (PRD) of TDP-43 and quantified their toxicity in yeast cells. Surprisingly, mutations that increase hydrophobicity and aggregation strongly decrease toxicity. In contrast, toxic variants promote the formation of dynamic liquid-like condensates. Mutations have their strongest effects in a hotspot that genetic interactions reveal to be structured in vivo, illustrating how mutagenesis can probe the in vivo structures of unstructured proteins. Our results show that aggregation of TDP-43 is not harmful but protects cells, most likely by titrating the protein away from a toxic liquid-like phase.",
        "method_text": "Variants for TDP-43 were constructed using a \"doped\" oligo for each of the TDP-43 libraries (290-331 and 332-373). Libraries were transformed in Saccharomyces cerevisiae and TDP-43 expression was induced for 5-6 generations. Variant counts were processed with DiMSum (Faure et al. 2020) to obtain a toxicity score for each variant. \r\nSee Bolognesi et al. 2019 for details.",
        "short_description": "Deep mutational scanning of TDP-43 prion-like domain using a toxicity assay.",
        "title": "TDP-43 toxicity",
        "keywords": [
            {
                "text": "intrisic disorder"
            },
            {
                "text": "prion-like domain"
            },
            {
                "text": "TDP-43"
            },
            {
                "text": "toxicity"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-12101-z",
                "url": "https://doi.org/10.1038/s41467-019-12101-z",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31519910",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31519910",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-9712-9163",
            "0000-0002-6632-947X"
        ],
        "scoresets": [
            "urn:mavedb:00000060-a-1",
            "urn:mavedb:00000060-a-2"
        ],
        "experimentset": "urn:mavedb:00000060"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-w",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 22, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 22 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 22 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-w-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-d",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.",
        "method_text": "A Deep Mutational Scan of TPK1 (thiamin pyrophosphokinase) using functional complementation in yeast was performed using DMS-TileSeq and a machine-learning method was used to impute the effects of missing variants and refine measurements of lower confidence. See [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for details.",
        "short_description": "A Deep Mutational Scan of human thiamin pyrophosphokinase (TPK1) using functional complementation in yeast.",
        "title": "TPK1 yeast complementation",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP109119",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP109119",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "scoresets": [
            "urn:mavedb:00000001-d-1",
            "urn:mavedb:00000001-d-2"
        ],
        "experimentset": "urn:mavedb:00000001"
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2020-12-10",
        "urn": "urn:mavedb:00000051-c",
        "publish_date": "2020-12-10",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study mutated the residues on GpA helix region of the bacterial inner membrane. The experiment links the insertion and self-association property of the tested region to the survive of bacteria and studied the membrane-protein energetics landscape of missense mutations of the target.",
        "method_text": "The helix region of GpA is used as the membrane-spanning segment for dsT$\\beta$L in this experiment. The authors created forward and reverse primers of lengths 40-85 base pairs with the central codon replaced by NNS which encodes all possible amino acid substitutions on the target sequence. They leveraged a traditional assay, the TOXCAT-$\\beta$-lactamase (T$\\beta$L) screen, and adapted it to deep mutational scanning studies (dsT$\\beta$L). The tested sequence is expressed in between a chimera of ToxR dimerization-dependent transcriptional activator of a chloramphenicol-resistance gene and $\\beta$-lactamase. In this construct, the membrane integration of target sequence determines the bacterial resistance to ampicillin and the self-association correlates with the chloramphenicol resistance. Besides, the orientation to the membrane of this chimera is also crucial for survival. The selection result was determined by deep-sequencing using Illumina.",
        "short_description": "A deep mutational scanning experiment targeting the GpA helix region on the bacterial inner membrane.",
        "title": "Helix region of Glycophorin A (GpA)",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.12125",
                "url": "https://doi.org/10.7554/eLife.12125",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "26824389",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26824389",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000051-c-1"
        ],
        "experimentset": "urn:mavedb:00000051"
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000047-a",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CCR5 and to map ligand interaction sites. Cells were selected for CCR5 surface expression.",
        "method_text": "Two libraries were generated independently by overlapping PCR using primers with an NNK codon, as described by Procko et al, 2013 and transfected into human Expi293F cells (a cell line lacking CCR5) using pCEP4.\r\nThe CCR5 combinatorial library was sorted for surface receptor expression by anti-myc staining.\r\nReplicates from one library used anti-myc-FITC and the other used anti-myc-Alexa 647.\r\nCell sorting was performed using a BD FACSAria II.\r\nTotal RNA was extracted and PCR-amplified before sequencing by Illumina MiSeq v3 or HiSeq 2500. \r\nTwo replicate selections were performed for each library (four total replicates).\r\n\r\nRaw data available from GEO under accession [GSE100368](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100368).",
        "short_description": "Deep mutational scan selecting for cell surface expression of CCR5 in Expi293F cells.",
        "title": "CCR5 surface expression",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "scoresets": [
            "urn:mavedb:00000047-a-1"
        ],
        "experimentset": "urn:mavedb:00000047"
    },
    {
        "creation_date": "2021-10-03",
        "modification_date": "2021-10-03",
        "urn": "urn:mavedb:00000081-a",
        "publish_date": "2021-10-03",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study aimed to functionally characterize BRCA1 missense variants at scale in order to provide the additional information necessary for more definitive interpretation of VUSs in the clinic. To do so, the authors performed a DMS on the RING and BRCT domains of BRCA1 for the ability to perform homology-directed DNA repair.",
        "method_text": "Hemagglutinin (HA)-tagged BRCA1 N-terminal HindIII-EcoRI fragment containing amino acids 1–302 was cloned into the plasmid pUC18. BRCA1 variant libraries were constructed in two pools, corresponding to amino-acid residues 2-96 and 97-192, using NNK-codon mutagenesis. The mutagenized HA-BRCA1 fragments were then ligated into a modified version of vector pcDNA5/FRT-TO at the BRCA1 cDNA EcoRI and HindIII sites. Barcodes, in the form of 16-base oligonucleotides, were then inserted at another multiple cloning site. \r\n\r\nThe libraries were transfected into HeLa-DR-FRT cells. HeLa-DR-FRT cells were derived from HeLa-DR cells described in Ransburgh et al. 2010 and have integrated a flippase recognition target (FRT) sequence from the pFRT/lacZeo plasmid (Thermo Fisher Scientific) as a landing pad. HeLa-DR-FRT cells are a reporter cell line such that it contains two inactive GFP-encoding alleles in its genome. Transfection and expression of an I-Scel endonuclease would induce a double-stranded DNA break in a site-specific manner at one of the inactive GFP alleles. Homology-directed repair (HDR), if functional, would use the other inactive GFP allele as template to correct and activate the broken GFP allele. Thus, if HDR is successful, the cell convert from GFP-negative to GFP-positive.\r\n\r\nCells transfected with the BRCA1 libraries were treated with siRNA against endogenous BRCA1 and pCBASceI to induce double-stranded breaks as described above. Then, the cells were sorted using FACS and genomic DNA was collected. Barcodes and sample indices were sequenced using a Nextseq 500 High Output 75 base kit.",
        "short_description": "BRCA1 RING and BRCT domains assayed for homology-directed DNA repair function.",
        "title": "BRCA1 RING and BRCT domains in homology-directed DNA repair",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE116427",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116427",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30219179",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30219179",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2072-3436"
        ],
        "scoresets": [
            "urn:mavedb:00000081-a-1"
        ],
        "experimentset": "urn:mavedb:00000081"
    },
    {
        "creation_date": "2022-03-18",
        "modification_date": "2022-06-14",
        "urn": "urn:mavedb:00000096-a",
        "publish_date": "2022-06-14",
        "created_by": "0000-0001-5034-1952",
        "modified_by": "0000-0001-5034-1952",
        "extra_metadata": {},
        "abstract_text": "This study assessed the activity of human glucokinase (GCK) variants using functional complementation. The hxk1Δhxk2Δglk1Δ yeast strain shows reduced growth on glucose medium which is rescued by expression of human GCK. The growth of yeast cells expressing GCK variants on 0.2% glucose medium was used as a read-out of GCK activity.",
        "method_text": "The GCK sequence was divided into three regions that were mutagenized, assayed and sequenced in parallel. Each regional variant library was constructed by POPCode mutagenesis using pooled oligos each containing a central degenerate NNK codon. \r\nGCK variant activity was assayed using yeast complementation.\r\nVariants were sequenced using the TileSeq approach on an Illumina NextSeq550.\r\nThe two replicates pre-selection were taken from the same pool of yeast transformants, while the two replicates post-selection were derived from the same pool of yeast transformants that were selected for GCK activity separately.",
        "short_description": "Activity of GCK variants measured by functional complementation of an hxk1Δhxk2Δglk1Δ yeast strain.",
        "title": "GCK activity measured by complementation",
        "keywords": [
            {
                "text": "GCK"
            },
            {
                "text": "GCK-MODY"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE198878",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198878",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-5034-1952",
            "0000-0001-7281-5696"
        ],
        "scoresets": [
            "urn:mavedb:00000096-a-1"
        ],
        "experimentset": "urn:mavedb:00000096"
    },
    {
        "creation_date": "2019-02-27",
        "modification_date": "2020-11-20",
        "urn": "urn:mavedb:00000049-a",
        "publish_date": "2020-11-20",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "Deep mutational scan of human MTHFR based on functional complementation in yeast, at three different concentrations of folate (12, 25 and 100 ug/ml ) and in two genetic backgrounds (WT / A222V)",
        "title": "MTHFR DMS",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390",
            "0000-0002-9219-4310",
            "0000-0002-2550-2141",
            "0000-0001-6465-5776"
        ],
        "scoresets": [
            "urn:mavedb:00000049-a-4",
            "urn:mavedb:00000049-a-6",
            "urn:mavedb:00000049-a-1",
            "urn:mavedb:00000049-a-5",
            "urn:mavedb:00000049-a-2",
            "urn:mavedb:00000049-a-3",
            "urn:mavedb:00000049-a-7",
            "urn:mavedb:00000049-a-8"
        ],
        "experimentset": "urn:mavedb:00000049"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-k",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The expression level of alpha-synuclein missense variants was determined by cell sorting of yeast expressing each variant fused to GFP.",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Expression Level in Yeast",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41589-020-0480-6",
                "url": "https://doi.org/10.1038/s41589-020-0480-6",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32152544",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32152544",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-k-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2022-08-24",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-a",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "A pooled, virally delivered, doxycycline-induced, cDNA expression library containing all 19 amino acid substitutions at residues 2–360 of ERK2 generated with Mutagenesis by Integrated TilEs (MITE) and transduced into BRAFV600E mutatant A375 cells. Selected in a pooled competition assay, where LOF ERK2 mutants are enriched relative to those with wild-type activity and GOF mutants depleted.\r\nScore is an average of 4 replicates normalized to the total reads per lane and log2 transformed\r\n\r\nReference early time point",
        "short_description": "Phenotypic Characterization of a Comprehensive Set of 6,810 MAPK1/ERK2 Missense Mutants",
        "title": "MAPK1 Early Time Point",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "scoresets": [
            "urn:mavedb:00000103-a-1"
        ],
        "experimentset": "urn:mavedb:00000103"
    },
    {
        "creation_date": "2019-02-18",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000011-a",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This was the first dataset described that used the EMPIRIC approach (\"extremely methodical and parallel investigation of randomized individual codons\"). It generated experimental fitness measurements for a nine amino acid region of yeast Hsp90. The experimental design is based on calculating growth rates for yeast containing variant Hsp90 sequences as compared to yeast containing the wild type sequence.",
        "method_text": "Fully randomized codons (NNN codons) were generated for each position and inserted into plasmids using a cassette ligation strategy. These plasmids were transformed into yeast carrying a temperature-sensitive copy of Hsp90 (G170D). After being grown up at the permissive temperature of 25C, the transformed population was heated in a water bath to inactivate G170D Hsp90 and then grown at 36C. Time points for Illumina sequencing were taken at 12, 24, 36, 48, 60, 72, and 84h time points.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90.",
        "title": "Deep mutational scan of HSP90",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "21464309",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/21464309",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000011-a-1"
        ],
        "experimentset": "urn:mavedb:00000011"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-n",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 17, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 17 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 17 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-n-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2022-08-26",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-c",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "A pooled, virally delivered, doxycycline-induced, cDNA expression library containing all 19 amino acid substitutions at residues 2–360 of ERK2 generated with Mutagenesis by Integrated TilEs (MITE) and transduced into BRAFV600E mutatant A375 cells. Selected in a pooled competition assay, where LOF ERK2 mutants are enriched relative to those with wild-type activity and GOF mutants depleted.\r\nScore is an average of 6 replicates normalized to the total reads per lane and log2 transformed\r\n\r\nInduced with DOX and selected with 2 microM SCH772984",
        "short_description": "Phenotypic Characterization of a Comprehensive Set of 6,810 MAPK1/ERK2 Missense Mutants. \r\nInduced with DOX and selected with 2 microM SCH772984",
        "title": "MAPK1 SCH772984",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "scoresets": [
            "urn:mavedb:00000103-c-1"
        ],
        "experimentset": "urn:mavedb:00000103"
    },
    {
        "creation_date": "2021-03-10",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000062-b",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the impact of CYP2C19 variants on the abundance of this protein in HEK293T. The authors fused the target protein with green fluorescent protein (GFP) and used the intensity of GPF as the indicator of target protein abundance.",
        "method_text": "This study used nicking mutagenesis method and generated CYP2C19 variant library which contained 121 missense mutations for each. Target protein was linked with green fluorescent protein (GFP) and co-expressed with mCherry as control. The variant library was introduced to HEK293T cells by a landing pad. After 5 days' growth, the cells were sorted to 4 bins by FACS according to the relative intensity of GFP and mCherry, and the variant frequency in each bin was determined by high-throughput sequencing which was then used to calculate the abundance score for each variant. The experiments are repeated four times.",
        "short_description": "This study tested the protein abundance of CYP2C19 variants by fusing green fluorescent protein.",
        "title": "Abundance of CYP2C19 variants",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1111/cts.12758",
                "url": "https://doi.org/10.1111/cts.12758",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32004414",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32004414",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000062-b-1"
        ],
        "experimentset": "urn:mavedb:00000062"
    },
    {
        "creation_date": "2020-12-14",
        "modification_date": "2020-12-20",
        "urn": "urn:mavedb:00000053-a",
        "publish_date": "2020-12-20",
        "created_by": "0000-0002-2866-3880",
        "modified_by": "0000-0002-2866-3880",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scanning (DMS) enables data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering (SPINE) as a programmable DMS technique. We validate SPINE with a reference single mutant dataset in the PSD95 PDZ3 domain and then characterize most pairwise double mutants to study epistasis. We observe wide-spread proximal negative epistasis, which we attribute to mutations affecting thermodynamic stability, and strong long-range positive epistasis, which is enriched in an evolutionarily conserved and function-defining network of ‘sector’ and clade-specifying residues. Conditional neutrality of mutations in clade-specifying residues compensates for deleterious mutations in sector positions. This suggests that epistatic interactions between these position pairs facilitated the evolutionary expansion and specialization of PDZ domains. We propose that SPINE provides easy experimental access to reveal epistasis signatures in proteins that will improve our understanding of the structural basis for protein function and adaptation.",
        "method_text": "The bacterial two-hybrid assay is based on PDZ3 binding to the CRIPT ligand. PDZ3 variants with a high affinity for the CRIPT ligand will recruit RNA polymerase α-subunit initiating expression of chloramphenicol acetyltransferase. This is a positive selection for highly functional PDZ3 variants. This system replicates the work of Salinas et al. (DOI: 10.7554/eLife.34300) and all plasmid and cell reagents were received as a gift from Rama Ranganathan. Plasmid was purified from cells before selection and after selection and the region covering the PDZ3 sequence was PCR amplified for 12 cycles with Illumina sequencing adapters. Amplicon DNA was purified with 1% agarose gel. Libraries were sequenced using Illumina MiSEQ in 150 bp paired-end configuration.",
        "short_description": "Bacterial two-hybrid assay to measure binding fitness of PSD95 PDZ3 domain to the CRIPT peptide ligand",
        "title": "Pairwise mutation fitness of PSD95 PDZ3 domain",
        "keywords": [
            {
                "text": "Binding"
            },
            {
                "text": "PDZ"
            },
            {
                "text": "SPINE mutagenesis"
            },
            {
                "text": "DMS"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2866-3880",
            "0000-0001-7609-4873"
        ],
        "scoresets": [
            "urn:mavedb:00000053-a-2",
            "urn:mavedb:00000053-a-1"
        ],
        "experimentset": "urn:mavedb:00000053"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000068-b",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors leveraged CRISPR-Cas9 technique to construct cell lines without wild type TP53 expression (p53NULL) in A549 human lung carcinoma. These cell lines are later transferred with p53 mutant library in order to study the function of these variants. This study used nutlin-3 which interrupts a negative regulator of p53 during the selection process. This paper was using an older version of TP53 reference sequence, and we are depositing the result according to the latest reference sequence.",
        "method_text": "This study used Mutagenesis by Integrated TilEs (MITE) method to generate the TP53 variant library which includes all single position missense and nonsense mutations as well as synonymous mutants. The p53Null cell line is infected with this library and cultured with nutlin-3 for 12 days. Variant frequency before and after selection are determined by Hiseq4000.",
        "short_description": "TP53 saturation mutagenesis screens with TP53 null cell line using nutlin-3 which interrupts a negative regulator of p53",
        "title": "Mutated p53 with nutlin-3",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1038/s41588-018-0204-y",
                "url": "https://doi.org/10.1038/s41588-018-0204-y",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "30224644",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30224644",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000068-b-1"
        ],
        "experimentset": "urn:mavedb:00000068"
    },
    {
        "creation_date": "2018-10-14",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000004-a",
        "publish_date": "2018-12-03",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study identified multiple gain-of-function mutations in the ubiquitination factor E4B U-box domain by measuring auto-ubiquitination in a phage display system. E4B is an E3 ligase, responsible for transferring a ubiquitin from an E2 ligase to the target (in this case the phage displaying E4B). Many of these mutations are not specific to one E2 enzyme and so may be generalizable for mutiple E2s and E3s.",
        "method_text": "The variant library was constructed using doped oligo synthesis, with a 2% error rate, corresponding to 0.225% of incorporating each incorrect base at each position. The phage display was performed using T7 phage and selected for Flag-Ub binding to anti-Flag beads. Full-length variant sequences were associated with 18-base DNA barcodes using the subassembly method [Hiatt et al.]. Barcodes were sequenced and counted for each of four time points in two replicates, and the barcode counts were used to quantify variant enrichment/depletion.",
        "short_description": "Deep mutational scan of the murine E4B (Ube4b) U-box domain using a phage display auto-ubiquitination assay.",
        "title": "Deep mutational scan of E4B (Ube4b) U-box domain auto-ubiquitination",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "U-box"
            },
            {
                "text": "E3"
            },
            {
                "text": "Phage display"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "ubiquitin"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "20081835",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/20081835",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23509263",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23509263",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2870-5099"
        ],
        "scoresets": [
            "urn:mavedb:00000004-a-1",
            "urn:mavedb:00000004-a-2",
            "urn:mavedb:00000004-a-3"
        ],
        "experimentset": "urn:mavedb:00000004"
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000079-a",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of pyrrolidine ketide synthase (PyKS) whose wildtype has low protein stability. The PyKS single mutation library is generated with the fluorescent protein GFP fused and selected by FACS. Mutants with high protein stability will have higher fluorescence intensity.",
        "method_text": "The variant library in this study is generated using nicking mutagenesis with NNK primers and expressed in E.col. Variants were generated in five non-overlapping tiles, covering residues 8-78, 79-156, 157-234, 235-312, and 313-388 (UniProt coordinates).\r\n\r\nCells were sorted using FACS on a BD Influx cell sorter into a reference population and a selected population, where the selected population were in the top 8-10% of GFP intensity. Variant counts in each population were determined by deep sequencing on an Illumina MiSeq with 250bp paired-end reads.",
        "short_description": "Selecting on pyrrolidine ketide synthase (PyKS) with higher protein stability by GFP fusing.",
        "title": "Stability selection of PyKS",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30721031",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30721031",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000079-a-1"
        ],
        "experimentset": "urn:mavedb:00000079"
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2020-12-10",
        "urn": "urn:mavedb:00000051-b",
        "publish_date": "2020-12-10",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study mutated the residues on ErbB2 helix region of the bacterial inner membrane. The experiment links the insertion and self-association property of the tested region to the survive of bacteria and studied the membrane-protein energetics landscape of missense mutations of the target.",
        "method_text": "The helix region of ErbB2 is used as the membrane-spanning segment for dsT$\\beta$L in this experiment. The authors created forward and reverse primers of lengths 40-85 base pairs with the central codon replaced by NNS which encodes all possible amino acid substitutions on the target sequence. They leveraged a traditional assay, the TOXCAT-$\\beta$-lactamase (T$\\beta$L) screen, and adapted it to deep mutational scanning studies (dsT$\\beta$L). The tested sequence is expressed in between a chimera of ToxR dimerization-dependent transcriptional activator of a chloramphenicol-resistance gene and $\\beta$-lactamase. In this construct, the membrane integration of target sequence determines the bacterial resistance to ampicillin and the self-association correlates with the chloramphenicol resistance. Besides, the orientation to the membrane of this chimera is also crucial for survival. The selection result was determined by deep-sequencing using Illumina.",
        "short_description": "A deep mutational scanning experiment targeting ErbB2 helix region on the bacterial inner membrane.",
        "title": "Helix region of ErbB2",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.12125",
                "url": "https://doi.org/10.7554/eLife.12125",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "26824389",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26824389",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000051-b-1"
        ],
        "experimentset": "urn:mavedb:00000051"
    },
    {
        "creation_date": "2020-06-18",
        "modification_date": "2020-06-19",
        "urn": "urn:mavedb:00000044-b",
        "publish_date": "2020-06-19",
        "created_by": "0000-0001-6713-6904",
        "modified_by": "0000-0001-6713-6904",
        "extra_metadata": {},
        "abstract_text": "The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance. See the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) for more information.",
        "method_text": "We constructed duplicate libraries of mutant variants of the SARS-CoV-2 receptor binding domain (RBD), and cloned the library into a yeast surface-display platform. We used FACS-seq assays to determine variant expression and binding scores: 1) We labeled RBD variants for cell surface expression levels (a correlate of folding stability), and/or binding of soluble ACE2 ligand across a range of ACE2 concentrations. 2) We used FACS to partition our library into bins of expression or binding. 3) We sequenced the variants from within each bin. 4) From the distribution of sequence reads across FACS bins, we can reconstruct each variant's mean expression. 5) For binding values, by comparing binding as a function of ACE2 concentration, we calculate binding constants from per-variant titration curves.\r\n\r\nWe provide our duplicate library measurements at the level of individual variants within our library, which are described by unique molecular identifier barcodes downstream from the variant RBD coding sequence. We also provide decomposed single-mutant scores, which are the primary mutation scores we use in our analysis of the data. In each of these datasets, the binding score is a delta-log<sub>10</sub>(_K_<sub>D,app</sub>) metric from the variant titration curves, and the expression score is a delta-log(mean fluorescence intensity) measurement of cell surface expression. Both metrics are relative to the unmutated SARS-CoV-2 reference sequence phenotype, polarized such that a positive value indicates higher affinity or expression compared to unmutated SARS-CoV-2, and a negative value indicates decreased affinity or expression compared to unmutated SARS-CoV-2.\r\n\r\nSee the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) or [GitHub repository](https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS) for additional information.",
        "short_description": "This experiment measures the effects on binding of variants and individual mutations in the SARS-CoV-2 RBD",
        "title": "Effects on expression of mutations in the SARS-CoV-2 RBD",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA639956",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA639956",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6713-6904",
            "0000-0001-9278-3644",
            "0000-0003-1267-3408"
        ],
        "scoresets": [
            "urn:mavedb:00000044-b-2",
            "urn:mavedb:00000044-b-1"
        ],
        "experimentset": "urn:mavedb:00000044"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000022-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of IRF6 enhancer in HaCaT cells.",
        "title": "Saturation mutagenesis MPRA of IRF6 enhancer",
        "keywords": [
            {
                "text": "IRF6"
            },
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444722",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444722",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000022-a-1"
        ],
        "experimentset": "urn:mavedb:00000022"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-c",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "Degenerate primers and recombination-based cloning were used to create a mutant library of the Fis1p TA protein in a Gal4-sfGFP-Fis1p plasmid. Cells with wild-type-like TA variants would fail to grow, since the Gal4 is localized to the mitochondrial membrane instead of in the nucleus to drive transcription on selective media. Sequencing was performed using a MiSeq Nano (2x150v2).\r\n\r\nThis experiment compares the population grown on supplemented minimal medium (SMM) -Trp -His medium with 5mM 3-aminotriazole to the baseline population grown on synthetic complete (SC) -Trp.",
        "short_description": "Deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium with 5mM 3-aminotriazole.",
        "title": "Fis1 tail anchor, SMM -Trp -His with 5mM 3-AT",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000076-c-1"
        ],
        "experimentset": "urn:mavedb:00000076"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-t",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 20, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 20 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 20 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-t-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000029-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of SORT1 enhancer in HepG2 cells.",
        "title": "Saturation mutagenesis MPRA of SORT1 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "SORT1"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444732",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444732",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444730",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444730",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000029-a-1",
            "urn:mavedb:00000029-a-2"
        ],
        "experimentset": "urn:mavedb:00000029"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-x",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 22, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 22 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 22 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-x-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000031-b",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of TERT promoter in glioblastoma SF7996 (GBM) cells.",
        "title": "Saturation mutagenesis MPRA of TERT promoter, GBM",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "TERT"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444734",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444734",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000031-b-1"
        ],
        "experimentset": "urn:mavedb:00000031"
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-c",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.",
        "method_text": "A Deep Mutational Scan of Calmodulin (*CALM1*) using functional complementation in yeast was performed using DMS-TileSeq and a machine-learning method was used to impute the effects of missing variants and refine measurements of lower confidence. See [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for details.",
        "short_description": "A Deep Mutational Scan of human Calmodulin using functional complementation in yeast.",
        "title": "Calmodulin yeast complementation",
        "keywords": [
            {
                "text": "sumoylation"
            },
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP109119",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP109119",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "scoresets": [
            "urn:mavedb:00000001-c-1",
            "urn:mavedb:00000001-c-2"
        ],
        "experimentset": "urn:mavedb:00000001"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-f",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 12h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 12h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-f-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-0",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "Meta-analysis of urn:mavedb:00000097-a-1, urn:mavedb:00000097-b-1, urn:mavedb:00000097-c-1, urn:mavedb:00000097-d-1, urn:mavedb:00000097-e-1 and 21 others",
        "title": "Meta-analysis of urn:mavedb:00000097-a-1, urn:mavedb:00000097-b-1, urn:mavedb:00000097-c-1, urn:mavedb:00000097-d-1, urn:mavedb:00000097-e-1 and 21 others",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [],
        "scoresets": [
            "urn:mavedb:00000097-0-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-d",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 16 µg/mL ampicillin at 37C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 16 µg/mL ampicillin at 37C",
        "title": "VIM-2 16 µg/mL AMP at 37C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-d-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000023-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of LDLR promoter in HepG2 cells.",
        "title": "Saturation mutagenesis MPRA of LDLR promoter",
        "keywords": [
            {
                "text": "LDLR"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444724",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444724",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000023-a-1",
            "urn:mavedb:00000023-a-2"
        ],
        "experimentset": "urn:mavedb:00000023"
    },
    {
        "creation_date": "2018-06-25",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000002-a",
        "publish_date": "2018-07-10",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This was the first published deep mutational scan. The experiment quantified binding affinity between the human YAP65 (YAP1) WW domain and a peptide binding partner using phage display. The phage display selection was tuned such that the enrichment in each round was moderate, allowing inefficient binders to be maintained in the population and subsequently quantified.",
        "method_text": "The target sequence was a codon-optimized human YAP65 WW domain. The variant library was constructed using doped oligo synthesis, with 0.7% of each non-target base at each position. The phage display was performed using T7 phage and selection for binding to biotinylated GTPPPPYTVG peptide attached to streptavidin-coated magnetic beads. Paired-end Illumina sequencing was performed such that both forward and reverse reads fully overlapped the variable region.",
        "short_description": "Deep mutational scan of the hYAP65 WW domain using phage display.",
        "title": "YAP65 WW domain",
        "keywords": [
            {
                "text": "WW domain"
            },
            {
                "text": "Phage display"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "Binding"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP002725",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP002725",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23035249",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23035249",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "20711194",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/20711194",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-7614-1713"
        ],
        "scoresets": [
            "urn:mavedb:00000002-a-1",
            "urn:mavedb:00000002-a-2"
        ],
        "experimentset": "urn:mavedb:00000002"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-b",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "Degenerate primers and recombination-based cloning were used to create a mutant library of the Fis1p TA protein in a Gal4-sfGFP-Fis1p plasmid. Cells with wild-type-like TA variants would fail to grow, since the Gal4 is localized to the mitochondrial membrane instead of in the nucleus to drive transcription on selective media. Sequencing was performed using a MiSeq Nano (2x150v2).\r\n\r\nThis experiment compares the population grown on supplemented minimal medium (SMM) -Trp -His medium with 10mM 3-aminotriazole to the baseline population grown on synthetic complete (SC) -Trp.",
        "short_description": "Deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium with 10mM 3-aminotriazole.",
        "title": "Fis1 tail anchor, SMM -Trp -His with 10mM 3-AT",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000076-b-1"
        ],
        "experimentset": "urn:mavedb:00000076"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000026-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of MYC enhancer (rs11986220) in LNCaP cells with 100nM DHT.",
        "title": "Saturation mutagenesis MPRA of MYC enhancer (rs11986220)",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "MYC"
            },
            {
                "text": "rs11986220"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444726",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444726",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000026-a-1"
        ],
        "experimentset": "urn:mavedb:00000026"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-c",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Miconazole",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-c-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-d",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 3, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 3 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 3 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-d-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000016-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of FOXE1 promoter in HeLa cells.",
        "title": "Saturation mutagenesis MPRA of FOXE1 promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "FOXE1"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444716",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444716",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000016-a-1"
        ],
        "experimentset": "urn:mavedb:00000016"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000020-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of HNF4A promoter in HEK293T cells.",
        "title": "Saturation mutagenesis MPRA of HNF4A promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "HNF4A"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444720",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444720",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000020-a-1"
        ],
        "experimentset": "urn:mavedb:00000020"
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-c",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection. \r\n\r\nThis record describes the selection performed on VIM-2 at 128 µg/mL ampicillin at 37C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 128 µg/mL ampicillin at 37C",
        "title": "VIM-2 128 µg/mL AMP at 37C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-c-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2021-11-01",
        "modification_date": "2021-11-02",
        "urn": "urn:mavedb:00000085-a",
        "publish_date": "2021-11-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 β-lactamase gene in *Escherichia coli* on different backgrounds. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "The variant library was constructed using PFunkel comprehensive codon mutagenesis. One NNN-containing mutagenic primer was used per codon.\r\n\r\nThis dataset describes variants on the TEM-19 background, which differs from TEM-1 by p.Gly236Ser (TEM-1 position not Ambler position).\r\n\r\nThe band-pass selection system is described in (Sohka et al., 2009). Briefly, cells are plated on media containing Tet and a variable concentration of Amp. If TEM-1 activity is too low for the Amp concentration, cells will not proliferate. If TEM-1 activity is too high, no cell wall damage will occur and TetC (which confers Tet resistance) will not be produced. Therefore cells should only grow if the TEM-1 variant’s activity level matches the Amp concentration.\r\n\r\nSequencing was performed using PacBio.",
        "short_description": "TEM-19 (TEM-1 variant) fitness on Amp.",
        "title": "TEM-19 Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "27173379",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27173379",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000085-a-1"
        ],
        "experimentset": "urn:mavedb:00000085"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-f",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the presence of the antibiotic to perform the selection. \r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations on cefotaxime resistance at 0.15 μg/ml",
        "title": "TEM-1 0.15 μg/ml cefotaxime",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-f-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-c",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 6h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 6h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-c-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2020-06-18",
        "modification_date": "2020-06-19",
        "urn": "urn:mavedb:00000044-a",
        "publish_date": "2020-06-19",
        "created_by": "0000-0001-6713-6904",
        "modified_by": "0000-0001-6713-6904",
        "extra_metadata": {},
        "abstract_text": "The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance. See the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) for more information.",
        "method_text": "We constructed duplicate libraries of mutant variants of the SARS-CoV-2 receptor binding domain (RBD), and cloned the library into a yeast surface-display platform. We used FACS-seq assays to determine variant expression and binding scores: 1) We labeled RBD variants for cell surface expression levels (a correlate of folding stability), and/or binding of soluble ACE2 ligand across a range of ACE2 concentrations. 2) We used FACS to partition our library into bins of expression or binding. 3) We sequenced the variants from within each bin. 4) From the distribution of sequence reads across FACS bins, we can reconstruct each variant's mean expression. 5) For binding values, by comparing binding as a function of ACE2 concentration, we calculate binding constants from per-variant titration curves.\r\n\r\nWe provide our duplicate library measurements at the level of individual variants within our library, which are described by unique molecular identifier barcodes downstream from the variant RBD coding sequence. We also provide decomposed single-mutant scores, which are the primary mutation scores we use in our analysis of the data. In each of these datasets, the binding score is a delta-log<sub>10</sub>(_K_<sub>D,app</sub>) metric from the variant titration curves, and the expression score is a delta-log(mean fluorescence intensity) measurement of cell surface expression. Both metrics are relative to the unmutated SARS-CoV-2 reference sequence phenotype, polarized such that a positive value indicates higher affinity or expression compared to unmutated SARS-CoV-2, and a negative value indicates decreased affinity or expression compared to unmutated SARS-CoV-2.\r\n\r\nSee the [preprint](https://www.biorxiv.org/content/10.1101/2020.06.17.157982v1) or [GitHub repository](https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS) for additional information.",
        "short_description": "This experiment measures the effects on binding of variants and individual mutations in the SARS-CoV-2 RBD",
        "title": "Effects on binding of mutations in the SARS-CoV-2 RBD",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA639956",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA639956",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6713-6904",
            "0000-0001-9278-3644",
            "0000-0003-1267-3408"
        ],
        "scoresets": [
            "urn:mavedb:00000044-a-1",
            "urn:mavedb:00000044-a-2"
        ],
        "experimentset": "urn:mavedb:00000044"
    },
    {
        "creation_date": "2022-08-23",
        "modification_date": "2022-08-23",
        "urn": "urn:mavedb:00000100-a",
        "publish_date": "2022-08-23",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study characterized the effect of single-codon insertion and deletion events on the function of TEM-1 beta-lactamase in the presence of varying concentrations of ampicillin.",
        "method_text": "The library of mutants containing all possible nucleotide insertion was generated using a degenerate NNN nucleotide sequence at teh 5’ end of the forward primer and a compatible reverse primer. TEM-1 variants were expressed on a pSkunk2 plasmid. The insertion mutants were characterized using three libraries, one for each third of the gene. The selection was performed using a band-pass genetic circuit, set up such that the cells will only grow if the activity of the TEM-1 variant protein matches the concentration of Amp present. If the activity is too low or too high for the Amp concentration, the cells will fail to grow. High-throughput sequencing was performed using Illumina MiSeq 300-bp paired-end reads.",
        "short_description": "Effect of single-codon insertions on TEM-1 fitness",
        "title": "TEM-1 single-codon insertions",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31034887",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31034887",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000100-a-1"
        ],
        "experimentset": "urn:mavedb:00000100"
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2020-12-04",
        "urn": "urn:mavedb:00000051-a",
        "publish_date": "2020-12-02",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-2449-7034",
        "extra_metadata": {},
        "abstract_text": "This study mutated the residues on CLS helix region of the bacterial inner membrane. The experiment links the insertion and self-association property of the tested region to the survive of bacteria and studied the membrane-protein energetics landscape of missense mutations of the target.",
        "method_text": "The C-terminal of L-Selectin is used as the membrane-spanning segment for dsT$\\beta$L in this experiment. The authors created forward and reverse primers of lengths 40-85 base pairs with the central codon replaced by NNS which encodes all possible amino acid substitutions on the target sequence. They leveraged a traditional assay, the TOXCAT-$\\beta$-lactamase (T$\\beta$L) screen, and adapted it to deep mutational scanning studies (dsT$\\beta$L). The tested sequence is expressed in between a chimera of ToxR dimerization-dependent transcriptional activator of a chloramphenicol-resistance gene and $\\beta$-lactamase. In this construct, the membrane integration of target sequence determines the bacterial resistance to ampicillin and the self-association correlates with the chloramphenicol resistance. Besides, the orientation to the membrane of this chimera is also crucial for survival. The selection result was determined by deep-sequencing using Illumina.",
        "short_description": "A deep mutational scanning experiment targeting the CLS helix region on the bacterial inner membrane.",
        "title": "C-terminal of L-Selectin (CLS)",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.12125",
                "url": "https://doi.org/10.7554/eLife.12125",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "26824389",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26824389",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000051-a-1"
        ],
        "experimentset": "urn:mavedb:00000051"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000068-a",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors leveraged CRISPR-Cas9 technique to construct cell lines with wild type TP53 expression (p53WT) in A549 human lung carcinoma. These cell lines are later transferred with p53 mutant library in order to study the function of these variants in the background of wildtype TP53. This study used nutlin-3 which interrupts a negative regulator of p53 during the selection process. This paper was using an older version of TP53 reference sequence, and we are depositing the result according to the latest reference sequence.",
        "method_text": "This study used Mutagenesis by Integrated TilEs (MITE) method to generate the TP53 variant library which includes all single position missense and nonsense mutations as well as synonymous mutants. The p53WT cell line is infected with this library and cultured with nutlin-3 for 12 days. Variant frequency before and after selection are determined by Hiseq4000.",
        "short_description": "TP53 saturation mutagenesis screens with TP53 wild-type using nutlin-3 which interrupts a negative regulator of p53",
        "title": "Mutated p53 paired with wildtype under nutlin-3",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1038/s41588-018-0204-y",
                "url": "https://doi.org/10.1038/s41588-018-0204-y",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "30224644",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30224644",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000068-a-1"
        ],
        "experimentset": "urn:mavedb:00000068"
    },
    {
        "creation_date": "2021-08-16",
        "modification_date": "2021-08-16",
        "urn": "urn:mavedb:00000066-a",
        "publish_date": "2021-08-16",
        "created_by": "0000-0001-6465-5776",
        "modified_by": "0000-0001-6465-5776",
        "extra_metadata": {},
        "abstract_text": "GDI1 variant effect map (Abstract - to be updated)",
        "method_text": "GDI1 variant effect map (Method - to be updated)",
        "short_description": "GDI1 variant effect map (Short description - to be updated)",
        "title": "GDI1 variant effect map",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6465-5776"
        ],
        "scoresets": [
            "urn:mavedb:00000066-a-1"
        ],
        "experimentset": "urn:mavedb:00000066"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000027-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of PKLR promoter, 24h post-transfection in K562 cells.",
        "title": "Saturation mutagenesis MPRA of PKLR promoter, 24h",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "PKLR"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444728",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444728",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000027-a-1"
        ],
        "experimentset": "urn:mavedb:00000027"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000090-a",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "To characterize the contributions of mutants to binding specificity of PDZ, the authors performed a deep mutation scan of PDZ3 from Rat DLG4 for binding to CRIPT and to T-2F.",
        "method_text": "Deep mutational scan of Rat DLG4 PDZ3 domain (311-393aa) was selected for binding to CRIPT by bacteria two-hybrid in *E. coli*. The mutation library was generated by NNS PCR.",
        "short_description": "Deep mutational scan of Rat DLG4 PDZ3 for binding to CRIPT.",
        "title": "PDZ3 domain binding to CRIPT",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23041932",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23041932",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000090-a-1"
        ],
        "experimentset": "urn:mavedb:00000090"
    },
    {
        "creation_date": "2019-07-10",
        "modification_date": "2019-07-15",
        "urn": "urn:mavedb:00000035-a",
        "publish_date": "2019-07-15",
        "created_by": "0000-0002-4998-4368",
        "modified_by": "0000-0002-4998-4368",
        "extra_metadata": {},
        "abstract_text": "Coronary heart disease (CHD) is a leading cause of death worldwide. The risk of CHD can be reduced by LDL-cholesterol-lowering medications called statins that potently inhibit HMG-CoA reductase (HMGCR), the enzyme that catalyzes the rate-limiting reaction of the mevalonate pathway. Proactive maps of human HMGCR may be able to model patient response to statins and identify the statin with the greatest likelihood of efficacy.",
        "method_text": "The yeast-based assay of HMGCR is a functional complementation assay that assesses the ability of human HMGCR to rescue the growth of an hmg1 hmg2 double deletion yeast strain in glucose media (Basson et al. 1988). We followed the TileSeq approach (Weile & Sun et al, MSB, 2017) to produce variant effect maps of HMGCR in glucose media without a statin, and media supplemented with atorvastatin or rosuvastatin.",
        "short_description": "A deep mutational scan of human HMG-CoA reductase (HMGCR) based on a functional complementation assay in yeast.",
        "title": "HMGCR yeast complementation",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-4998-4368"
        ],
        "scoresets": [
            "urn:mavedb:00000035-a-2",
            "urn:mavedb:00000035-a-3",
            "urn:mavedb:00000035-a-1"
        ],
        "experimentset": "urn:mavedb:00000035"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-p",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 18, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 18 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 18 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-p-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-g",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the absence of antibiotic. Two replicate selections were performed.\r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations under no selection",
        "title": "TEM-1 unselected",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-g-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-07",
        "urn": "urn:mavedb:00000040-a",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of variants in yeast HSP90 under different combinations of temperature (30C or 36C) and presence/absence of salt (0.5 M NaCl). The results explore the adaptive potential of this essential gene.",
        "method_text": "Fully randomized codons (NNN codons) were generated for each position and inserted into plasmids using a cassette ligation strategy. Yeast were grown in a dextrose shutoff strain, which grows normally on galactose but turns off expression of endogenous HSP90 in dextrose media. Cells were grown in galactose media to near saturation, after which they were grown on dextrose for 8 hours before being split into four cultures, one for each experimental condition. Time points for Illumina sequencing were taken during the experiment at different times based the overall growth rate of that condition.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under different combinations of temperature and salinity.",
        "title": "Deep mutational scan of HSP90 varying temperature and salt",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24299404",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24299404",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000040-a-1",
            "urn:mavedb:00000040-a-2",
            "urn:mavedb:00000040-a-3",
            "urn:mavedb:00000040-a-4"
        ],
        "experimentset": "urn:mavedb:00000040"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-e",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 4, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 4 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 4 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-e-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2018-07-10",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000003-b",
        "publish_date": "2018-07-10",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "These experiments measured the functional consequences of mutations in the BRCA1 RING domain, where most clinically-relevant single nucleotide variants reside. One goal of the study was to create a \"look-up table\" of single nucleotide variants for clinical use, by prospectively measuring the impact of all possible variants that are likely to appear in patients. The study combines two different assays - one based on E3 ubiquitin ligase activity and one based on BRCA1-BARD1 heterodimer formation - and makes one of the first attempts to combine data from different MAVEs on the same target.\r\n\r\nThis entry contains scores from the yeast two-hybrid assay, which tested the BRCA1-BARD1 heterodimer formation in BRCA1 variants.",
        "method_text": "Variants were constructed using PALS (Programmed Allelic Series) [Hiatt et al.]. Full-length variant sequences were associated with 16-base DNA barcodes using the subassembly method [Kitzman et al.]. Barcodes were sequenced and counted for each of four time points (0h, 16h, 41h, 64h) in three replicates, and the barcode counts were used to quantify variant enrichment/depletion.",
        "short_description": "Deep mutational scan of the BRCA1 RING domain using a yeast two-hybrid heterodimerization assay.",
        "title": "BRCA1 Y2H",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "Yeast two-hybrid"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "RING domain"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "20081835",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/20081835",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "25559584",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25559584",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "25823446",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25823446",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2870-5099"
        ],
        "scoresets": [
            "urn:mavedb:00000003-b-2",
            "urn:mavedb:00000003-b-1"
        ],
        "experimentset": "urn:mavedb:00000003"
    },
    {
        "creation_date": "2021-10-31",
        "modification_date": "2021-10-31",
        "urn": "urn:mavedb:00000084-a",
        "publish_date": "2021-10-31",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study demonstrated the applicability of deep mutational scanning for inference of protein structural features (e.g. residue depth and active-site identity) and sequence-function relationships. A library of bacterial toxin CcdB variants was generated via site-directed mutagenesis. The library was then treated to induce expression at increasing levels, which were assigned rank numbers and these ranks were used to score each mutation.",
        "method_text": "Mutants were generated on plasmids using site-directed mutagenesis and transformed into the CcdB sensitive E. coli strain Top10pJAT. Transformed cells were plated on LB plates with seven concentrations of glucose (repressor) and arabinose (inducer). Because CcdB is toxic, only cells containing inactive variants will survive.\r\n\r\nCcdB DNA was isolated from each population and amplified by PCR using primers containing a 10-base long Multiplex IDentifier sequence tag (MID) that tagged the growth conditions. Tagged libraries were then pooled together and sequenced with the 454 GS FLX sequencer.",
        "short_description": "Deep mutational scan against CcdB toxicity in E. coli",
        "title": "CcdB toxicity",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22325784",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22325784",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2072-3436"
        ],
        "scoresets": [
            "urn:mavedb:00000084-a-1"
        ],
        "experimentset": "urn:mavedb:00000084"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-f",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Spermidine",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-f-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-j",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Tunicamycin",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-j-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2022-08-26",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-d",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "A pooled, virally delivered, doxycycline-induced, cDNA expression library containing all 19 amino acid substitutions at residues 2–360 of ERK2 generated with Mutagenesis by Integrated TilEs (MITE) and transduced into BRAFV600E mutatant A375 cells. Selected in a pooled competition assay, where LOF ERK2 mutants are enriched relative to those with wild-type activity and GOF mutants depleted.\r\nScore is an average of 6 replicates normalized to the total reads per lane and log2 transformed\r\n\r\nInduced with DOX and selected with 3 microM VRT-11E",
        "short_description": "Phenotypic Characterization of a Comprehensive Set of 6,810 MAPK1/ERK2 Missense Mutants. \r\nInduced with DOX and selected with 3 microM VRT-11E",
        "title": "MAPK1 VRT-11E",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "scoresets": [
            "urn:mavedb:00000103-d-1"
        ],
        "experimentset": "urn:mavedb:00000103"
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000048-a",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CXCR4 and to map ligand interaction sites. Cells were selected for CXCR4 surface expression.",
        "method_text": "The human CXCR4 sequence was generated by oligo assembly and fused to a c-myc tag. SSM libraries were generated by overlapping PCR using primers with an NNK codon, as described by Procko et al, 2013.\r\nThe SSM library was transfected into CXCR4-knockout human Expi293F cells using pCEP4. \r\nSurface receptor expression was measured by anti-myc staining and cells were sorted on a BD FACSAria II.\r\nTwo replicates each were performed with anti-myc-FITC and anti-myc-Alexa.\r\nTotal RNA was extracted and PCR-amplified before sequencing by Illumina MiSeq v 3 or HiSeq 2500. \r\n\r\nRaw data available from GEO under accession [GSE100368](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100368).",
        "short_description": "Deep mutational scan selecting for cell surface expression of CXCR4 in Expi293F cells.",
        "title": "CXCR4 surface expression",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "scoresets": [
            "urn:mavedb:00000048-a-1"
        ],
        "experimentset": "urn:mavedb:00000048"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000034-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of ZRS enhancer in NIH3T3 cells. Co-transfected with Hoxd13.",
        "title": "Saturation mutagenesis MPRA of ZRS enhancer, Hoxd13",
        "keywords": [
            {
                "text": "ZRS"
            },
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444737",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444737",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444815",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444815",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444814",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444814",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444813",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444813",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444908",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444908",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444907",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444907",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444906",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444906",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000034-a-1"
        ],
        "experimentset": "urn:mavedb:00000034"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000032-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of UC88 (ultraconserved element) enhancer in Neuro-2a cells.",
        "title": "Saturation mutagenesis MPRA of UC88 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "UC88"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444735",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444735",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000032-a-1"
        ],
        "experimentset": "urn:mavedb:00000032"
    },
    {
        "creation_date": "2019-02-17",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000010-a",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the sequence-function relationships for variants in a common, eukaryotic RNA binding domain, the RRM2 domain of yeast Pab1. The results identified clusters of residues with similar mutational patterns as well as highly-conserved residues that are critical for stability and/or function.",
        "method_text": "Mutants were tested by measuring the ability of Pab1 genes containing variants in RRM2 to complement *pab1*$\\Delta$. Variants were generated using doped oligo synthesis, with a 4% error rate. Variant RRM2 domains were sequenced such that the paired-end Illumina reads overlapped in the region of interest.",
        "short_description": "Deep mutational scan of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein (Pab1).",
        "title": "Deep mutational scan of Pab1 RRM domain",
        "keywords": [
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "RNA-binding"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24064791",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24064791",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000010-a-1"
        ],
        "experimentset": "urn:mavedb:00000010"
    },
    {
        "creation_date": "2021-09-16",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000069-a",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study used deep mutagenesis to identify ACE2 variants with increased binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein in a cell-based assay. Cells expressing ACE2 variants with high or low binding to RBD were sorted based on fluorescence detection of bound RBD fused to superfolder GFP (sfGFP) and myc-tagged ACE2 expression.",
        "method_text": "The cDNA of full-length human ACE2 tagged with N-terminal c-myc was diversified by site-saturation mutagenesis at 117 amino acid residues spanning the RBD-ACE2 interface and the substrate-binding cavity. This was accomplished by overlap extension PCR using primers with degenerate NNK codons. Human Expi293F cells were transfected with the plasmid library diluted with a large excess of carrier plasmid to yield no more than one coding variant per cell. The cell culture was incubated with 1/20 (replicate 1) or 1/40 (replicate 2) dilution of a medium containing RBD fused to superfolder GFP (sfGFP) at its C-terminus. Cells were co-stained with anti-myc Alexa 647 to quantify surface ACE2 expression. Bound RBD was subsequently measured relative to surface ACE2 expression. Cells with the highest (top 15%; “nCoV-S-High” sort) and lowest (bottom 20%; “nCoV-S-Low” sort) levels of bound RBD-sfGFP relative to ACE2 expression were collected by fluorescence activated cell sorting (FACS). Transcripts in the sorted populations were extracted, diversified ACE2 regions were PCR amplified and Illumina sequenced.",
        "short_description": "ACE2 variants with highest or lowest binding affinity to the SARS-CoV-2 spike protein.",
        "title": "ACE2 binding to SARS-CoV-2 spike protein",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE147194",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147194",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32753553",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32753553",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-1494-8030"
        ],
        "scoresets": [
            "urn:mavedb:00000069-a-1",
            "urn:mavedb:00000069-a-2"
        ],
        "experimentset": "urn:mavedb:00000069"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2022-01-22",
        "urn": "urn:mavedb:00000093-a",
        "publish_date": "2021-12-23",
        "created_by": "0000-0002-7160-7753",
        "modified_by": "0000-0002-7160-7753",
        "extra_metadata": {},
        "abstract_text": "BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino- terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a Mammalian 2-hybrid assay. Downstream of the laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that 15%-20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 45 with concordant computational and functional assay evidence in favor of pathogenicity plus 223 with concordant evidence in favor of benignity; these are particularly likely to be classified as Likely Pathogenic and Likely Benign, respectively, once human observational data become available.",
        "method_text": "Pre-set analysis choices.\r\nA number of key analysis parameters were set before the resulting analyses were conducted. These included:\r\n1. Calibration would be based on some sort of multivariate logistic regression using human\r\nobservational data, and excluding computational or functional assay data.\r\n2. The calibration set of RING domain sequence variants used inclusion thresholds of published\r\nhuman observational data having Posterior probability of pathogenicity (Post_P)<0.10, or Post_P>0.90, starting from an assumed BRCA1/2 key domain prior probability in favor of pathogenicity (Prior_P) of 0.35 (Easton et al., PMID: 17924331. Li et al., PMID: 31853058).\r\n3. Because the calibration set had more pathogenic than benign calibrant variants, it was decided in advance to include the two presumed benign variants extracted from our existing protein multiple sequence alignment: p.K45R and p.C91H (Tavtigian et al., PMID: 18951461).\r\nConsiderations #2 and #3 resulted in a set of 30 “calibration series” sequence variants (Table 1), 29 missense substitutions and one in-frame deletion. One of these, c.211A>G (p.R71G) was excluded from calibration because our prior analyses predicted that it would damage mRNA splicing and then it was shown to be pathogenic on that basis (Vallee et al., PMID: 26913838. Parsons et al., Parsons et al., PMID: 31131967)\r\nReporter cell line for the Mammalian 2-hybrid assay.\r\nA HEK293 cell line was prepared with two GAL4-responsive M2H reporters, one with ZsGreen readout and blasticidin resistance, and the other with Tdtomato and puromycin resistance.\r\n\r\nBRCA1 RING domain variant library generation.\r\nPlasmid libraries containing the variants to assay in the multiplexed format were generated using a HiFi assembly-based cloning strategy. We developed three different backbone vectors, based on pBIND (E245A; Promega) for cloning three 100 bp sections of the BRCA1 RING domain. Each backbone encoded the complete BRCA1 RING domain (amino acids 1-100, plus an additional 84 aa) fused to the GAL4 DNA binding domain, and the three vectors together allow mutagenesis of the entire RING domain. Following the GAL4 sequence, we inserted a P2A sequence followed by a BFP sequence. The BFP acts as a proxy for productive BRCA1 expression and allows gating on a tight range of BRCA1 expression during the sort step of the M2H assay. Oligonucleotide pools representing the three thirds of the ring domain were synthesized by Twist Bioscience with the following features: 1) the missense substitutions and in-frame indels to be tested; 2) each missense substitution or in-frame indel was synthesized with 4 different pairs of silent substitutions that acted as a barcode identifier (8 different 2 nt barcodes were designed for each third of the RING domain, with the silent substitutions chosen from alternate nucleotides that are wt in a non-human primate); 3) 5’ and 3’ sequence tails for HiFi assembly. Barcode combinations with the wildtype peptide sequence were generated for each barcode used, and synthesized at a 3:1 ratio to variants in the oligo pool to insure capture of all wildtype-barcode combinations in the assay. The oligo pool was amplified (12 cycles) in three separate reactions using primer sets corresponding to 5’ and 3’ ends of the three thirds of the ring domain, with the resulting amplified pools representing each third. Each amplified pool was cloned en masse into the corresponding backbone vector using NEB HiFi assembly mastermix (E2621) and transformed. Single colonies were picked and arrayed in a 96-well format for individual plasmid preps (Invitrogen) and resulting plasmid DNAs re-arrayed into the inner 60- wells of a 96-well plate (to avoid edge effects in the subsequent transfections), and then diluted to 25 ng/μl.\r\n\r\nThe BARD1 RING domain, encoded within the first 200 amino acids, fused to HA, was cloned into a modified pACT vector (E246A, Promega), with the VP16 sequence moved distal to the BARD1 coding sequence, to create a C-terminal fusion. Similar to the BRCA1-GAL4 construct, following the VP16 sequence, we inserted a P2A sequence followed by zsYellow sequence for gating purposes.\r\nMultiplexed mammalian 2-hybrid assay.\r\nIndividual transfection reactions for each plasmid were set up with 20,000 reporter cells per well and 50 ng of pACT_BARD1:zsYELLOW plus 50 ng of the corresponding BRCA1-GAL4:BFP plasmid (1:1 molar ratio) from the dilution plates described in the previous section. 48 hours post-infection, cells were harvested, pooled, and FACs sorted on a BD 5 laser FACSAria. The strategy relied first on gating a narrow range of zsYellow+/BFP+ to ensure evaluation of only cells productively transfected with both plasmids, and to limit the range of BRCA1-GAL4 and BARD1-VP16 expression. Gated cells were sorted into one of six bins based on increasing expression of both the dtTomato and zsGreen reporters. RNA was isolated from each bin using the Direct-zol RNA miniprep kit (Zymo Research); bins with less than 1 X106 cells were adjusted to 1 X106 with HEK293 cells to insure uniformity in RNA isolation. Total RNA was converted to cDNA using the SuperScript VILO cDNA Synthesis Kit (Invitrogen). The RING sequence of BRCA1 was then isolated by RT-PCR using primers corresponding to sequence 5 bp 5’ of the intron engineered into the BRCA1 construct and nucleotides 305-330 of the BRCA1 CDS. Sequencing libraries were prepared using the Ovation Ultralow Library System (NUGEN # 0344NB-A01), excluding the end-repair step and using a different barcode for each of the bins. The libraries were sequenced on an Illumina MiSeq channel using the MiSeq 300 bp Cycle Paired-end sequencing protocol. Each paired-end read set was combined into one read using FLASH 25 and aligned to an index containing the individual BRCA1-RING domain variant sequences with barcodes using Novoalign. We counted each alignment as positive only if there was a perfect match along the 427 bp length of the amplicon. The distribution of positive counts exhibited a discontinuity at about 2,000, with values above 2,000 forming a smooth curve. The frequency of counts below 2,000 declined sharply, suggesting a threshold effect. Accordingly, we restricted further analyses to variant-barcode combinations with counts above 2,000; these were tabulated resulting in the counts per bin (1-6) data for each individual variant-barcode assayed, which was one of the input tables for the statistical analyses.",
        "short_description": "We tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for its effect on heterodimerization with BARD1 in a Mammalian 2-hybrid assay.  The assay data collected were calibrated, validated, and integrated with other available data to arrive at clinically applicable classifications.  About 89% of the missense substitutions could be assigned clinical classifications with about 20% being pathogenic.",
        "title": "Functional Evaluation of BRCA1 RING Domain Missense Substitutions",
        "keywords": [
            {
                "text": "RING domain"
            },
            {
                "text": "protein binding"
            },
            {
                "text": "FACS"
            },
            {
                "text": "Deep mutational scanning"
            },
            {
                "text": "Flow Cytometry"
            },
            {
                "text": "Alanine-scanning"
            },
            {
                "text": "Mammalian two-hybrid"
            },
            {
                "text": "heteroduplex"
            },
            {
                "text": "In-frame deletion-scanning"
            },
            {
                "text": "Proline-scanning"
            },
            {
                "text": "ACMG AMP variant classification"
            },
            {
                "text": "Calibration"
            },
            {
                "text": "Validation"
            },
            {
                "text": "regression"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1101/092619",
                "url": "http://doi.org/10.1101/092619",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-7160-7753"
        ],
        "scoresets": [
            "urn:mavedb:00000093-a-1"
        ],
        "experimentset": "urn:mavedb:00000093"
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-25",
        "urn": "urn:mavedb:00000102-0",
        "publish_date": "2022-08-25",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "",
        "short_description": "Meta-analysis of urn:mavedb:00000013-a-1, urn:mavedb:00000101-a-1",
        "title": "Meta-analysis of urn:mavedb:00000013-a-1, urn:mavedb:00000101-a-1",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "scoresets": [
            "urn:mavedb:00000102-0-1"
        ],
        "experimentset": "urn:mavedb:00000102"
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000048-b",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CXCR4 and to map ligand interaction sites. Cells were selected for binding to the CXCR4 physiological ligand CXCL12.",
        "method_text": "The human CXCR4 sequence was generated by oligo assembly and fused to a c-myc tag. SSM libraries were generated by overlapping PCR using primers with an NNK codon, as described by Procko et al, 2013.\r\nThe SSM library was transfected into CXCR4-knockout human Expi293F cells using pCEP4. \r\nSurface receptor expression was measured by anti-myc-Alexa staining and cells were sorted on a BD FACSAria II.\r\nCells were incubated with CXCL12 fused to superfolder GFP (sf-GFP) and sorted for interaction with CXCL12-sfGFP. \r\nTotal RNA was extracted and PCR-amplified before sequencing by Illumina MiSeq v 3 or HiSeq 2500. \r\n\r\nRaw data available from GEO under accession [GSE100368](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100368).",
        "short_description": "Deep mutational scan selecting for CXCR4 binding to CXCL12 in Expi293F cells.",
        "title": "CXCR4 CXCL12 binding",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "scoresets": [
            "urn:mavedb:00000048-b-1"
        ],
        "experimentset": "urn:mavedb:00000048"
    },
    {
        "creation_date": "2021-09-29",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-g",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 0.5 µg/mL cefotaxime at 37C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 0.5 µg/mL cefotaxime at 37C",
        "title": "VIM-2 0.5 µg/mL CTX at 37C",
        "keywords": [
            {
                "text": "cefotaxime"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-g-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2019-07-10",
        "modification_date": "2019-07-15",
        "urn": "urn:mavedb:00000036-a",
        "publish_date": "2019-07-15",
        "created_by": "0000-0002-4998-4368",
        "modified_by": "0000-0002-4998-4368",
        "extra_metadata": {},
        "abstract_text": "Coronary heart disease (CHD) is a leading cause of death worldwide. A major risk factor of CHD is high low-density lipoprotein cholesterol (LDL-C), which is the defining feature of familial hypercholesterolemia, a genetic disorder characterized by mutations in genes involved in cholesterol uptake, such as LDLRAP1. Proactive maps of LDLRAP1 may identify pathogenic variation of autosomal recessive hypercholesterolemia (ARH) for early diagnosis of ARH.",
        "method_text": "The yeast-based assay of LDLRAP1 is a yeast two-hybrid assay that assesses the ability of human LDLRAP1 to interact with protein partners, which would activate the expression of HIS3 to allow histidine production and the growth of a yeast strain in selective media lacking histidine (Fields and Song 1989). We followed the TileSeq approach (Weile & Sun et al, MSB, 2017) to produce variant effect maps of LDLRAP1 based on its interaction with OBFC1 or AP2B1.",
        "short_description": "A deep mutational scan of low-density lipoprotein receptor adaptor protein 1 (LDLRAP1) based on a yeast two-hybrid assay.",
        "title": "LDLRAP1 Y2H",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-4998-4368"
        ],
        "scoresets": [
            "urn:mavedb:00000036-a-1",
            "urn:mavedb:00000036-a-2"
        ],
        "experimentset": "urn:mavedb:00000036"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-d",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Melatonin",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-d-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-a",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with MG-132",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-a-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2022-02-22",
        "modification_date": "2022-06-17",
        "urn": "urn:mavedb:00000094-a",
        "publish_date": "2022-06-17",
        "created_by": "0000-0002-6394-7715",
        "modified_by": "0000-0002-6394-7715",
        "extra_metadata": {},
        "abstract_text": "Clinical exome sequencing has yielded extensive disease-related missense single-nucleotide variants (SNVs) with uncertain significance, leading to diagnostic uncertainty. KCNQ4 is one of the most commonly responsible genes for autosomal dominant non-syndromic hearing loss. According to the gnomAD cohort, approximately 1 in 100 people harbor missense variants in KCNQ4 (only variants with minor allele frequency < 0.1% were included), but most are of unknown consequence. To prospectively characterize the function of all 4,085 possible missense SNVs of human KCNQ4, we recorded the whole-cell currents using patch-clamp and categorized 1,059 missense SNVs as loss-of-function. Further, to mimic the heterozygous condition in DFNA2 (Deafness non-syndromic autosomal dominant 2) patients, we co-expressed 1,059 loss-of-function variants with wild-type KCNQ4, of which 501 variants exerted dominant-negative effects. Our functional classification is highly concordant with the auditory phenotypes in Kcnq4 mutant mice and the assessments of pathogenicity in clinical variant interpretations. Taken together, our results can provide functional evidence to support the pathogenicity classification of newly discovered KCNQ4 missense variants in clinical genetic testing.",
        "method_text": "Whole-cell current amplitude scores at +40 mV for all missense SNVs of KCNQ4 were normalized by whole-cell current of WT KCNQ4 at +40 mV.  Only variants that contained at least three replicates are included. Variants with whole-cell current amplitude score less than 0.54 were classified as current-reduced variants. Variants with whole-cell current amplitude score more than 2.08 were classified as current-increased variants.\r\nContinuous curves were generated by plotting the normalized tail current against membrane potentials using the Boltzmann function I/Imax = 1/(1+ (exp(V1/2-Vm)k)), where I is the magnitude of the tail current, Imax is the maximum current magnitude, V1/2 is the half-activation voltage, Vm is the membrane potential, and k = RT/zF is the slope factor. Only variants that contained at least three replicates are included. Variants with shifted V1/2 more than +10 mV were classified as LOF. Variants with shifted V1/2 more than -10 mV were classified as GOF.\r\nThen  to mimic the effect of KCNQ4 variants in heterozygous DFNA2 patients and determine the dominant-negative effects, 1,059 LOF mutants and 114 GOF mutants were co-transfected with wild-type KCNQ4.",
        "short_description": "Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4",
        "title": "Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6394-7715",
            "0000-0001-8460-831X",
            "0000-0003-4714-2076"
        ],
        "scoresets": [
            "urn:mavedb:00000094-a-2",
            "urn:mavedb:00000094-a-3",
            "urn:mavedb:00000094-a-4",
            "urn:mavedb:00000094-a-5",
            "urn:mavedb:00000094-a-6",
            "urn:mavedb:00000094-a-7",
            "urn:mavedb:00000094-a-10",
            "urn:mavedb:00000094-a-11",
            "urn:mavedb:00000094-a-8",
            "urn:mavedb:00000094-a-9",
            "urn:mavedb:00000094-a-1",
            "urn:mavedb:00000094-a-13",
            "urn:mavedb:00000094-a-12",
            "urn:mavedb:00000094-a-14",
            "urn:mavedb:00000094-a-15"
        ],
        "experimentset": "urn:mavedb:00000094"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000017-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of GP1BB promoter in HEL 92.1.7 cells.",
        "title": "Saturation mutagenesis MPRA of GP1BB promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "GP1BB"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444717",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444717",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000017-a-1"
        ],
        "experimentset": "urn:mavedb:00000017"
    },
    {
        "creation_date": "2021-04-12",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000064-a",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of _E.coli_ LamB which is the binding protein of phage &lambda; prion during infection. The bacteria are cultured in the media contains phage &lambda; and the growth rate for each mutant is determined to indicate its resistance to phage invasion.",
        "method_text": "The variant library in this study is generated by error-prone PCR and expressed in a lamB knockout _E.coli_ strain. The bacteria are cultured either in LB media as control group and LB with phage &lambda; as selection group. The frequency for each variant in those groups is determined by Illumina NextSeq using the Nextera kit.",
        "short_description": "Growth rate of E.coli with mutated LamB cultured with rich phage λ",
        "title": "LamB resistance to phage λ",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA604031",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA604031",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1099/mgen.0.000364",
                "url": "https://doi.org/10.1099/mgen.0.000364",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32238226",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32238226",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000064-a-1"
        ],
        "experimentset": "urn:mavedb:00000064"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000091-a",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "To search for possible secondary mutations that that can confer drug resistance in the context of BRAF V600E, the authors performed a deep mutation scan of human BRAF, selecting for enrichment in B3/F cells surviving vemurafenib treatment.",
        "method_text": "Saturation mutagenesis of 77 amino acids surrounding the PLX4720‐binding site. Eight mutant pools were generated—corresponding to amino acids 458–466, 467–476, 477–486, 501–510, 511–520, 527–536, 579–587, and 588–596—in which each amino acid was mutated to all possible 64 codons. The mutant pools were transferred into a retroviral vector containing BRAFV600E and then stably transduced into the human melanoma cell line A375.\r\n\r\nAfter transfection with mutant BRAF, cells were treated with vemurafenib. Cells surviving vemurafenib treatment were then sequenced to determine the enrichment of resistance mutations.",
        "short_description": "Deep mutational scan of the BRAF V600E allele for resistance to the cancer drug vemurafenib.",
        "title": "BRAF resistance to vemurafenib",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24112705",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24112705",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000091-a-1"
        ],
        "experimentset": "urn:mavedb:00000091"
    },
    {
        "creation_date": "2019-07-29",
        "modification_date": "2019-07-29",
        "urn": "urn:mavedb:00000038-a",
        "publish_date": "2019-07-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of single amino acid changes in ubiquitin on binding to E1 (Uba1). Combined with work from a previous study on the effect of ubiquitin mutations on yeast growth rate, this showed that ubiquitin-E1 binding was not linearly related to growth rate and that mutations in ubiquitin are likely to affect multiple function that modulate growth rate.",
        "method_text": "This experiment used the same library of ubiquitin variants as previously described in Roscoe et al. 2013. The ubiqutin variants were displayed as C-terminal fusions with Aga2-HA and reacted with E1. Bound cells were isolated using FACS and deep sequencing was used to quantify enrichment or depletion of cells in the bound population.",
        "short_description": "Deep mutational scan of ubiquitin measuring binding to E1 with yeast display with limiting E1.",
        "title": "Ubiquitin E1 binding, limiting E1",
        "keywords": [
            {
                "text": "Binding"
            },
            {
                "text": "FACS"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "E1"
            },
            {
                "text": "yeast display"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24862281",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24862281",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23376099",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23376099",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000038-a-1"
        ],
        "experimentset": "urn:mavedb:00000038"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-01-17",
        "urn": "urn:mavedb:00000057-d",
        "publish_date": "2021-01-17",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors used saturation mutagenesis to study the variant effect of Ras, on the oncogenic G12V background, without the regulation of GTPase activating protein (GAP) or guanine nucleotide exchange factor (GEF). The variants were selected by bacterial two-hybrid strategy.",
        "method_text": "The RAS mutant library was generated by oligonucleotide-directed mutagenesis on the oncogenic G12V background. The mutant library was transfected into bacteria without GAP or GEF expression and the functioning RAS protein which will bind to GTP as well as Raf. The binding of these molecules can trigger the transcription of an antibiotic resistant factor. The library was separated to three sub-libraries in order to cover the whole RAS gene length which ranges from the residue 2-56, 57-111, and 112-166. These samples were selected individually. The samples in different sub-libraries were barcoded and pooled together for MiSeq sequencing.",
        "short_description": "Selection on the oncogenic G12V mutated type of Ras",
        "title": "G12V mutated Ras",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28686159",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28686159",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000057-d-1"
        ],
        "experimentset": "urn:mavedb:00000057"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-y",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 23, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 23 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 23 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-y-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-b",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 4h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 4h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-b-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000031-c",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of TERT promoter in glioblastoma SF7996 (GBM) cells, siRNA knockdown of GABPA.",
        "title": "Saturation mutagenesis MPRA of TERT promoter, GBM siRNA knockdown",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "TERT"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444734",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444734",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000031-c-1"
        ],
        "experimentset": "urn:mavedb:00000031"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-g",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 24h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 24h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-g-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2019-02-14",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000012-a",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment demonstrated the programmed allelic series (PALS) method for site-directed mutagenesis using microarrays. The impact of nearly all singleton missense mutation in the Gal4 yeast transcription factor was measured in multiple selections.",
        "method_text": "Mutagenic PCR primers were synthesized on a DNA microarray and released into solution. These encoded all possible single amino acid changes in codons 2-65 of Gal4. Full length variants were tagged with random DNA barcodes. The relationship between barcode and variant was determined using synthetic long read subassembly sequencing.",
        "short_description": "Deep mutational scan of Gal4 DNA-binding domain using a yeast growth assay.",
        "title": "Deep mutational scan of Gal4 DNA-binding domain",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "DNA-binding"
            },
            {
                "text": "Yeast two-hybrid"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA268398",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA268398",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25559584",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25559584",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000012-a-1",
            "urn:mavedb:00000012-a-2",
            "urn:mavedb:00000012-a-3",
            "urn:mavedb:00000012-a-4",
            "urn:mavedb:00000012-a-5",
            "urn:mavedb:00000012-a-6"
        ],
        "experimentset": "urn:mavedb:00000012"
    },
    {
        "creation_date": "2021-03-10",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000062-a",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the impact of CYP2C9 variants on the abundance of this protein in HEK293T. The authors fused the target protein with green fluorescent protein (GFP) and used the intensity of GPF as the indicator of target protein abundance.",
        "method_text": "This study used nicking mutagenesis method and generated CYP2C9 variant library which contained 109 missense mutations for each. Target protein was linked with green fluorescent protein (GFP) and co-expressed with mCherry as control. The variant library was introduced to HEK293T cells by a landing pad. After 5 days' growth, the cells were sorted to 4 bins by FACS according to the relative intensity of GFP and mCherry, and the variant frequency in each bin was determined by high-throughput sequencing which was then used to calculate the abundance score for each variant. The experiments are repeated four times.",
        "short_description": "This study tested the protein abundance of CYP2C9 variants by fusing green fluorescent protein.",
        "title": "Abundance of CYP2C9 variants",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1111/cts.12758",
                "url": "https://doi.org/10.1111/cts.12758",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32004414",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32004414",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000062-a-1"
        ],
        "experimentset": "urn:mavedb:00000062"
    },
    {
        "creation_date": "2021-09-20",
        "modification_date": "2021-09-20",
        "urn": "urn:mavedb:00000071-b",
        "publish_date": "2021-09-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scanning was used on a library of 1.9x10^7 *Streptococcus pyogenes* Cas9 (SpCas9) variants to infer the effects of each mutation and screen for functional changes. A selection system in *E. coli* was established to differentiate between active and inactive mutant variants of SpCas9. The biological system used positive and negative selection to assay SpCas9 nuclease function in order to gather information about amino acids that allow SpCas9 to cleave DNA.",
        "method_text": "Negative selection plasmids US0hisB-pyrF- were used to perform selection of SpCas9 variants by generating electrocompetent cells. These cells were electroporated and plated on both selection and control plates. The SpCas9 mutant library was cloned and extrapolated to be transformed into positive and negative selection competent cells. Following recovery, the transformations were used to perform titrations for negative selection, positive selection, and controls. Specific mutant cloning was performed by generating overlapping fragments necessary to produce chosen mutation combinations. Following that, the cells were pooled together and analyzed using Flow cytometry on a Becton Dickinson FACSAria. Next generation sequencing was performed using an Illuman NextSeq using 2x150bp paired-end reads.",
        "short_description": "Negative (off-target) selection of SpCas9 in a bacterial selection system.",
        "title": "SpCas9 negative selection",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "SRP107783",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP107783",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29203891",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29203891",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000071-b-1"
        ],
        "experimentset": "urn:mavedb:00000071"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-f",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 4, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 4 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 4 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-f-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-l",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 16, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 16 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 16 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-l-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000025-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of MYC enhancer (rs6983267) in HEK293T cells.",
        "title": "Saturation mutagenesis MPRA of MYC enhancer (rs6983267)",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "rs6983267"
            },
            {
                "text": "MYC"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444727",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444727",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000025-a-1"
        ],
        "experimentset": "urn:mavedb:00000025"
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-25",
        "urn": "urn:mavedb:00000101-a",
        "publish_date": "2022-08-25",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment used massively parallel sequencing (VAMP-seq) to measure the abundance scores of new variants in the PTEN gene, as well as to validate abundance measurements for previously studied variants in the PTEN gene. The resulting PTEN abundance dataset demonstrates the ability of large-scale variant functional data paired with cancer genomics datasets and follow-up assays to understand how uncharacterized cancer-associated variants contribute to oncogenesis.",
        "method_text": "The variant library was constructed to supply variants missing in the original PTEN site saturation mutagenesis library. 198 positions with low coverage in the initial experiment were re-amplified using degenerate NNK primers. Resulting PTEN library was fused to EGFP and tagged with a unique nucleotide barcode. Illumina sequencing and library sorting experiments were performed as described in (Matreyek et al., 2018).",
        "short_description": "Amino acid scores for variant abundance by massively parallel sequencing (VAMP-seq) applied to PTEN (fill-in dataset).",
        "title": "PTEN VAMP-seq Fill-in",
        "keywords": [
            {
                "text": "VAMP-seq"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE159469",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159469",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "34649609",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/34649609",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "scoresets": [
            "urn:mavedb:00000101-a-1"
        ],
        "experimentset": "urn:mavedb:00000101"
    },
    {
        "creation_date": "2018-06-29",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-b",
        "publish_date": "2018-06-29",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.",
        "method_text": "A Deep Mutational Scan of SUMO1 using functional complementation in yeast was performed using DMS-TileSeq and a machine-learning method was used to impute the effects of missing variants and refine measurements of lower confidence. See [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for details.",
        "short_description": "A Deep Mutational Scan of the human SUMO1 using functional complementation in yeast.",
        "title": "SUMO1 yeast complementation",
        "keywords": [
            {
                "text": "sumoylation"
            },
            {
                "text": "imputation"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP109119",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP109119",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "scoresets": [
            "urn:mavedb:00000001-b-2",
            "urn:mavedb:00000001-b-1"
        ],
        "experimentset": "urn:mavedb:00000001"
    },
    {
        "creation_date": "2021-09-29",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-e",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 2 µg/mL ampicillin at 25C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 2 µg/mL ampicillin at 25C",
        "title": "VIM-2 2 µg/mL AMP at 25C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-e-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2018-07-10",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000003-a",
        "publish_date": "2018-07-10",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "These experiments measured the functional consequences of mutations in the BRCA1 RING domain, where most clinically-relevant single nucleotide variants reside. One goal of the study was to create a \"look-up table\" of single nucleotide variants for clinical use, by prospectively measuring the impact of all possible variants that are likely to appear in patients. The study combines two different assays - one based on E3 ubiquitin ligase activity and one based on BRCA1-BARD1 heterodimer formation - and makes one of the first attempts to combine data from different MAVEs on the same target.\r\n\r\nThis entry describes the phage autoubiquitination assay, which tested the E3 ubiquitin ligase activity of BRCA1 variants.",
        "method_text": "Variants were constructed using PALS (Programmed Allelic Series) [Hiatt et al.]. Full-length variant sequences were associated with 16-base DNA barcodes using the subassembly method [Kitzman et al.]. Barcodes were sequenced and counted for each of six time points in six replicates, and the barcode counts were used to quantify variant enrichment/depletion.",
        "short_description": "Deep mutational scan of the BRCA1 RING domain using a phage autoubiquitination assay.",
        "title": "BRCA1 E3",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "Phage display"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "RING domain"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "20081835",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/20081835",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "25559584",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25559584",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "25823446",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25823446",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2870-5099"
        ],
        "scoresets": [
            "urn:mavedb:00000003-a-2",
            "urn:mavedb:00000003-a-1"
        ],
        "experimentset": "urn:mavedb:00000003"
    },
    {
        "creation_date": "2019-08-07",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000039-a",
        "publish_date": "2019-08-07",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effects of yeast HSP90 variants under the control of different promoters to explore the relationship between protein sequence and expression level. The results showed that reduced expression level (compared to wild-type expression) revealed new partial loss of function mutations.",
        "method_text": "Fully randomized codons (NNN codons) were generated for each position and inserted into plasmids using a cassette ligation strategy. Constructs were generated with one of four constitutive promoters (GPD, TEF, ADH, or CYC), with or without the 3'UTR from the CYC gene. Constructs without the 3'UTR had the plasmid backbone as their UTR sequence, and are designated '$\\Delta$ter' or 'dter'. Yeast were grown in synthetic dextrose media lacking tryptophan. Time points for Illumina sequencing were taken at 12, 16, 20, 24, 32, 40, and 48 hours for GPD, TEF and TEF$\\Delta$ter, and at 16, 20, 24, 32, 40, and 48 hours for CYC, ADH, CYC$\\Delta$ter, and ADH$\\Delta$ter due to slower overall growth rates.",
        "short_description": "Deep mutational scan of all single mutants in a nine-amino acid region of Hsp90 (Hsp82) in Saccharomyces cerevisiae under the control of different promoters.",
        "title": "Deep mutational scan of HSP90 under multiple promoters",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23825969",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23825969",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000039-a-1",
            "urn:mavedb:00000039-a-2",
            "urn:mavedb:00000039-a-3",
            "urn:mavedb:00000039-a-4",
            "urn:mavedb:00000039-a-5",
            "urn:mavedb:00000039-a-6",
            "urn:mavedb:00000039-a-7"
        ],
        "experimentset": "urn:mavedb:00000039"
    },
    {
        "creation_date": "2021-04-12",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000064-b",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of _E.coli_ LamB which facilitates the transportation of maltodextrin. The bacteria are cultured in the media that maltodextrin is the only carbon source and the growth rate for each mutant is determined to indicate its impact on maltodextrin transportation function.",
        "method_text": "The variant library in this study is generated by error-prone PCR and expressed in a lamB knockout _E.coli_ strain. The bacteria are cultured either in media containing glucose as control group and media containing maltodextrin as the only carbon source as selection group. The frequency for each variant in those groups is determined by Illumina NextSeq using the Nextera kit.",
        "short_description": "Growth rate of E.coli with mutated LamB where maltodextrin is the sole carbon source",
        "title": "Maltose transportation of LamB",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA604031",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA604031",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1099/mgen.0.000364",
                "url": "https://doi.org/10.1099/mgen.0.000364",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32238226",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32238226",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000064-b-1"
        ],
        "experimentset": "urn:mavedb:00000064"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-h",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence for a CG-containing RNA-seq enhancer sequence.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, CG-containing RNA-seq enhancer sequence.",
        "title": "Exonic splicing for CG-containing enhancer",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-h-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-u",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 21, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 21 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 21 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-u-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-d",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence for an hnRNPA1 binding site (with upstream T).",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, hnRNPA1 binding site (with upstream T).",
        "title": "Exonic splicing for hnRNPA1 binding site",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-d-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000014-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of BCL11A enhancer in HEL 92.1.7 cells.",
        "title": "Saturation mutagenesis MPRA of BCL11A enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "BCL11A"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444714",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444714",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000014-a-1"
        ],
        "experimentset": "urn:mavedb:00000014"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-l",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Brefeldin A",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-l-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-d",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 8h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 8h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-d-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000075-a",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study presents a neutralization based assay to assess mutations’ in the E protein in the viral envelope of Zika Virus (ZIKV). E protein genes were used to detect variant interactions' effect on viral neutralization by monoclonal antibodies. DMS measured 9,576 possible amino acid mutations that contribute to 31,752 possible mutant codon sequences within the E protein. Variant infectivity was determined by a TCID50 assay.",
        "method_text": "Mutant plasmid libraries were created by cloning the entire E protein coding sequence into a single plasmid of Zika virus, strain MR766. \r\n\r\nMutagenesis was performed to generate single amino acid mutations on the E protein gene through NNN PCR. Three fully independent biological replicates were performed.\r\n\r\n293T cells were used to produce pools of virus genomes encoding all E protein mutants. Functional variants were selected by infecting Vero cells at low MOI. Input viruses were washed away and infection was allowed to continue for 3 or 4 rounds of additional infection, leading to enrichment of functional variants.\r\n\r\nViral RNA was extracted from the Vero cell population, reverse-transcribed, and sequenced using barcoded sub-amplicon sequencing.",
        "short_description": "Deep mutational scan of the Zika Virus E protein.",
        "title": "Zika E protein DMS",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA530795",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA530795",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31511387",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31511387",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000075-a-1"
        ],
        "experimentset": "urn:mavedb:00000075"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-z",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 23, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 23 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 23 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-z-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-e",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an hnRNP D binding site.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an hnRNP D binding site.",
        "title": "Exonic splicing for hnRNP D binding site",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-e-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000074-a",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Systematic mutagenesis was used to create a mutant library of Hsp82 (yeast Hsp90) genes from yeast across the gene to assess protein fitness.",
        "method_text": "Fully randomized codons (NNN codons) were generated for each position and inserted into plasmids using a cassette ligation strategy. \r\n\r\nThe assay was performed in p414ADHΔTER, which has a reduced level of Hsp82 and therefore sensitized the yeast.\r\n\r\nTwo biological replicates were performed for positions 12-21 and 92-101.",
        "short_description": "Yeast growth assay of Hsp82 (yeast Hsp90) covering the first 231 positions.",
        "title": "Yeast growth Hsp82 (Hsp90)",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "27068472",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27068472",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000074-a-1"
        ],
        "experimentset": "urn:mavedb:00000074"
    },
    {
        "creation_date": "2019-01-23",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000006-a",
        "publish_date": "2019-01-24",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study described the functional consequence of over 100,000 enhancer variants *in vivo* in mouse liver. Two human enhancers (ALDOB, ECR11) and one mouse enhancer (LTV1) were known to be active in mouse liver and therefore variants in these enhancers should show a measurable difference in transcription. The results were broadly consistent with evolutionary data and transcription factor binding sites, but were not always concordant demonstrating the importance of measuring the effect of enhancer variants directly.\r\n\r\nThis MaveDB entry describes the ALDOB enhancer data. Datasets for other enhancers described in the same publication are also available: [ECR11](https://www.mavedb.org/experiment/urn:mavedb:00000007-a/) [LTV1](https://www.mavedb.org/experiment/urn:mavedb:00000008-a/)",
        "method_text": "Variants were constructed using doped oligo with 1% of each non-target base included at each position (ratio of 97:1:1:1). Full-length enhancer haplotypes were assembled and cloned into tagged pGL4.23 plasmids. Each variant haplotype was tagged with a 20-bp sequence, with one tag per haplotype in almost all cases. Each single nucleotide change was present in at least 42 haplotypes. \r\n\r\nThe enhancers were injected into the mouse tail vein and mouse livers were harvested after 24h. RNA was isolated from fresh mouse livers, subjected to DNAseI treatment to remove any DNA contamination, reverse-transcribed into cDNA, and sequenced.\r\n\r\nTwo sets of sequencing reactions were performed. One used short Illumina reads (42 total cycles) to sequence the tag sequence used for quantifying each enhancer's activity. The other used subassembly synthetic long read sequencing to associate the tags with the full-length enhancer haplotypes.",
        "short_description": "Massively parallel functional dissection of the ALDOB enhancer in a mouse liver transcription assay.",
        "title": "Massively parallel functional dissection of ALDOB enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "liver"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRA049159",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRA049159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22371081",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22371081",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000006-a-1"
        ],
        "experimentset": "urn:mavedb:00000006"
    },
    {
        "creation_date": "2021-10-25",
        "modification_date": "2021-10-26",
        "urn": "urn:mavedb:00000082-a",
        "publish_date": "2021-10-26",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Scanning mutagenesis of bovine Arrestin-1 was performed to measure binding to the GPCR rhodopsin, to provide functional insight for cellular communication in higher organisms. This is primarily an alanine scanning dataset.",
        "method_text": "Mutations were introduced by PCR assisted by the AAscan program suite, 403 mutants of Arrestin-1 covering its complete sequence, 1-418. Arrestin mutants were expressed in E. coli in sets of 12, each including wild type as reference for relative expression levels. Arrestin-1 labelled by fusion to the fluorescent protein mCherry, which allowed binding experiments directly from Escherichia coli cell lysates.",
        "short_description": "Scanning mutagenesis of bovine Arrestin-1 for binding to GPCR rhodopsin.",
        "title": "Arrestin-1 binding",
        "keywords": [
            {
                "text": "GPCR"
            },
            {
                "text": "Alanine-scanning"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24449856",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24449856",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2289-7659"
        ],
        "scoresets": [
            "urn:mavedb:00000082-a-1"
        ],
        "experimentset": "urn:mavedb:00000082"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-i",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Rapamycin",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-i-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000090-b",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "To characterize the contributions of mutants to binding specificity of PDZ, the authors performed a deep mutation scan of PDZ3 from Rat DLG4 for binding to CRIPT and to T-2F.",
        "method_text": "Deep mutational scan of Rat DLG4 PDZ3 domain (311-393aa) was selected for binding to T-2F by bacteria two-hybrid in *E. coli*. The mutation library was generated by NNS PCR.",
        "short_description": "Deep mutational scan of Rat DLG4 PDZ3 for binding to T-2F.",
        "title": "PDZ3 domain binding to T-2F",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23041932",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23041932",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000090-b-1"
        ],
        "experimentset": "urn:mavedb:00000090"
    },
    {
        "creation_date": "2018-06-26",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000001-a",
        "publish_date": "2018-06-26",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.",
        "method_text": "A Deep Mutational Scan of UBE2I using functional complementation in yeast was performed using two different methods: DMS-BarSeq and DMS-TileSeq, both datasets were combined and a machine-learning method was used to impute the effects of missing variants and refine measurements of lower confidence. See [**Weile *et al.* 2017**](http://msb.embopress.org/content/13/12/957) for details.",
        "short_description": "A Deep Mutational Scan of the human SUMO E2 conjugase UBE2I using functional complementation in yeast.",
        "title": "UBE2I yeast complementation",
        "keywords": [
            {
                "text": "E2"
            },
            {
                "text": "sumoylation"
            },
            {
                "text": "imputation"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP109101",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP109101",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRP109119",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP109119",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29269382",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29269382",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "scoresets": [
            "urn:mavedb:00000001-a-2",
            "urn:mavedb:00000001-a-3",
            "urn:mavedb:00000001-a-4",
            "urn:mavedb:00000001-a-1"
        ],
        "experimentset": "urn:mavedb:00000001"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-i",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 15, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 15 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 15 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-i-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000019-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of HBG1 promoter in HEL 92.1.7 cells.",
        "title": "Saturation mutagenesis MPRA of HBG1 promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "HBG1"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444719",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444719",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000019-a-1"
        ],
        "experimentset": "urn:mavedb:00000019"
    },
    {
        "creation_date": "2020-11-11",
        "modification_date": "2020-11-11",
        "urn": "urn:mavedb:00000047-c",
        "publish_date": "2020-11-11",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilised site-saturation mutagenesis (SSM) to measure the functional consequences of mutations in the human chemokine receptor, CCR5 and to map ligand interaction sites. Cells were selected for binding to HIV-1~BaL~ gp120-CD4.",
        "method_text": "The CCR5 variant library was generated by overlapping PCR using primers with an NNK codon, as described by Procko et al, 2013 and transfected into human Expi293F cells (a cell line lacking CCR5) using pCEP4.\r\nCCR5 interactions with chemokines (CCL3, CCL4, CCL5) were unable to be characterised by deep mutational scanning. Instead, cells were selected for interaction with an important protein ligand, the HIV-1 Env subunit gp120 following incubation with HIV-1~BaL~ gp120 fused to CD4 domains D1-D2.\r\nSurface expression was measured using anti-myc-Alexa 647.\r\nCell sorting was performed using a BD FACSAria II.\r\nTotal RNA was extracted and PCR-amplified before sequencing by Illumina MiSeq v3 or HiSeq 2500 to quantify variants. \r\nTwo replicate selections were performed.\r\n\r\nRaw data available from GEO under accession [GSE100368](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100368).",
        "short_description": "Deep mutational scan selecting for CCR5 binding to HIV-1(BaL) gp120-CD4 in Expi293F cells.",
        "title": "CCR5 HIV binding",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29678950",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29678950",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23827138",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23827138",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0001-6681-7994"
        ],
        "scoresets": [
            "urn:mavedb:00000047-c-1"
        ],
        "experimentset": "urn:mavedb:00000047"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-k",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 16, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 16 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 16 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-k-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-i",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes the sequence for an AC-rich RNA-seq enhancer sequence.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, AC-rich RNA-seq enhancer sequence.",
        "title": "Exonic splicing for AC-rich enhancer",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-i-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000018-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of HBB promoter in HEL 92.1.7 cells.",
        "title": "Saturation mutagenesis MPRA of HBB promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "HBB"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444718",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444718",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000018-a-1"
        ],
        "experimentset": "urn:mavedb:00000018"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000028-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of RET enhancer in Neuro-2a cells.",
        "title": "Saturation mutagenesis MPRA of RET enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000028-a-1"
        ],
        "experimentset": "urn:mavedb:00000028"
    },
    {
        "creation_date": "2021-01-03",
        "modification_date": "2021-01-03",
        "urn": "urn:mavedb:00000054-a",
        "publish_date": "2021-01-03",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured variant lipid phosphatase activity using massively parallel functional testing with a humanised yeast assay. It measured the effects of PTEN mutation on lipid phosphatase activity in vivo, which is vital for preventing the accumulation of phospholipids, and is therefore required for cell survival.",
        "method_text": "Variant libraries were created using tiles and inverse PCR in a mutagenesis process similar to the mutagenesis integrated tiles (MITE) approach. PCR products were incorporated into plasmids using SLiCE-mediated recombination. Plasmid libraries were normalized and pooled to represent saturation mutagenesis for each quadrant of PTEN. p110$\\alpha$-CAAX-mediated selection was completed on each pool. Samples were then normalised, combined into a common pool, and sequenced across multiple runs using pair-ended 300 base-pair reads on Illumina MiSeq platform (v.3 reagent kit). Two biological replicates were performed, each with three technical replicate selections.",
        "short_description": "PTEN activity measured using a lipid phosphatase assay in a humanized yeast model.",
        "title": "PTEN Lipid Phosphatase",
        "keywords": [
            {
                "text": "phosphatase"
            },
            {
                "text": "humanized yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA437337",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA437337",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29706350",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29706350",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-9955-0656"
        ],
        "scoresets": [
            "urn:mavedb:00000054-a-1"
        ],
        "experimentset": "urn:mavedb:00000054"
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000078-b",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the impact of vitamin K epoxide reductase (VKOR) variants affecting protein abundance using VAMP-seq. The mutated VKOR are fused with eGFP and variants leading to misfolded proteins will cause a decrease in fluorescence intensity. The variant library is expressed in human HEK293T cells and selected by FACS to indicate the variant effects.",
        "method_text": "The variant is generated by mutagenesis primers through PCR which is barcoded and covers 92.5% of all possible variants. This library is introduced to HEK293T cells using a landing pad. The cell line also expresses mCherry from an internal ribosomal entry site as a control for protein expression. Individual cells are then sorted using FACS to four bins according to the relative intensity of eGFP and mCherry. Each bin is deeply sequenced and the final abundance scores are calculated.",
        "short_description": "VKOR protein stability measured by VAMP-seq.",
        "title": "VKOR protein stability",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE149922",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149922",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "PRJNA630502",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA630502",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32870157",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32870157",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000078-b-1"
        ],
        "experimentset": "urn:mavedb:00000078"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000031-d",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of TERT promoter in glioblastoma SF7996 (GBM) cells, siRNA scrambled control.",
        "title": "Saturation mutagenesis MPRA of TERT promoter, GBM siRNA control",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "TERT"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444734",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444734",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000031-d-1"
        ],
        "experimentset": "urn:mavedb:00000031"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000015-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of F9 promoter in HepG2 cells.",
        "title": "Saturation mutagenesis MPRA of F9 promoter",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "F9"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444715",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444715",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000015-a-1"
        ],
        "experimentset": "urn:mavedb:00000015"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2020-12-10",
        "urn": "urn:mavedb:00000052-b",
        "publish_date": "2020-12-10",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study generated thousands of mutated sequence on Gcn4 activation domain which contains one or several amino acid substitutions. They used a high-throughput fluorescent reporter assay to identify the transcription ability of mutated Gcn4 sequences through cell sorting in nutrient stress condition.",
        "method_text": "The designed mutated Gcn4 activation domain was combined to a synthetic transcription factor and expressed in yeast. The transcription factor is fused to mCherry and functioning transcription factor is able to facilitate the expression of GFP, which is the genome-integrated reporter gene. The cells are cultured under nutrient stress condition. Cells with distinct Gcn4 activity are sorted by fluorescence-activated cell sorting system to several bins according to the ratio of GFP and mCherry fluorescence. The cells are sorted into 8 bins: bin 1 with low GFP or mCherry level; bin 2 with low GFP level and normal mCherry level; and the other bins are evenly partitioned according to the ratio of the two fluorscence. The variant abundance is determined by high-throughput sequencing in an Illumina platform.",
        "short_description": "Mutagenesis study of Gcn4 activation domain in starvation media using fluorescent reporter assay.",
        "title": "Gcn4 activation domain induction ratio",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.17632/rbfr6m4733.1",
                "url": "https://doi.org/10.17632/rbfr6m4733.1",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "29525204",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29525204",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000052-b-1"
        ],
        "experimentset": "urn:mavedb:00000052"
    },
    {
        "creation_date": "2020-10-05",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000070-a",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 $\\beta$-lactamase gene in _Escherichia coli_. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "The variant library was constructed using PFunkel comprehensive codon mutagenesis. The gene was mutagenized and assayed as three sub-region (codons 1-96, 97-192, and 193-287). One NNN-containing mutagenic primer was used per codon. Library construction is described in detail in (Firnberg and Ostermeier, 2012), where the library used in these experiments is referred to as \"CCM-2.\"\r\n\r\nThe band-pass selection system is described in (Sohka et al., 2009). Briefly, cells are plated on media containing Tet and a variable concentration of Amp. If TEM-1 activity is too low for the Amp concentration, cells will not proliferate. If TEM-1 activity is too high, no cell wall damage will occur and TetC (which confers Tet resistance) will not be produced. Therefore cells should only grow if the TEM-1 variant's activity level matches the Amp concentration.\r\n\r\nSequencing was performed using 454 GS-FLX.",
        "short_description": "Experimental fitness of variants in the TEM-1 β-lactamase gene in the presence of ampicillin.",
        "title": "Experimental fitness of TEM-1 β-lactamase",
        "keywords": [
            {
                "text": "PFunkel"
            },
            {
                "text": "454 sequencing"
            },
            {
                "text": "band-pass selection"
            },
            {
                "text": "resistance"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000070-a-3",
            "urn:mavedb:00000070-a-4",
            "urn:mavedb:00000070-a-1",
            "urn:mavedb:00000070-a-2"
        ],
        "experimentset": "urn:mavedb:00000070"
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-i",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 2 µg/mL ampicillin at 37C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 2 µg/mL ampicillin at 37C",
        "title": "VIM-2 2 µg/mL AMP at 37C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-i-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-o",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 18, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 18 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 18 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-o-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2022-08-23",
        "modification_date": "2022-08-23",
        "urn": "urn:mavedb:00000100-b",
        "publish_date": "2022-08-23",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study characterized the effect of single-codon insertion and deletion events on the function of TEM-1 beta-lactamase in the presence of varying concentrations of ampicillin.",
        "method_text": "The library of mutants containing all possible nucleotide deletions was generated using a forward primer with a 3-base deletion on the 5’ end and a compatible reverse primer. TEM-1 variants were expressed on a pSkunk2 plasmid. The selection was performed using a band-pass genetic circuit, set up such that the cells will only grow if the activity of the TEM-1 variant protein matches the concentration of Amp present. If the activity is too low or too high for the Amp concentration, the cells will fail to grow. High-throughput sequencing was performed using PacBio.",
        "short_description": "Effect of single-codon deletions on TEM-1 fitness",
        "title": "TEM-1 single-codon deletions",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "31034887",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31034887",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000100-b-1"
        ],
        "experimentset": "urn:mavedb:00000100"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-e",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the presence of the antibiotic to perform the selection. Two replicate selections were performed.\r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 2500 μg/ml",
        "title": "TEM-1 2500 μg/ml Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-e-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000024-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of MSMB promoter in HEK293T cells.",
        "title": "Saturation mutagenesis MPRA of MSMB promoter",
        "keywords": [
            {
                "text": "MSMB"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444725",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444725",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000024-a-1"
        ],
        "experimentset": "urn:mavedb:00000024"
    },
    {
        "creation_date": "2020-06-26",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-h",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson's. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3' to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\n\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "A comprehensive library of 2,600 missense variants of the protein alpha-synuclein, which is implicated in Parkinson's disease, were screened for relative toxicity in yeast, a cellular model for alpha-synuclein pathobiology. Additional experiments were performed in chemically perturbed backgrounds, and relative expression level was determined by cell sorting based on the fluorescence of a fusion protein reporter.",
        "title": "Deep Mutational Scanning of alpha-Synuclein in Yeast",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41589-020-0480-6",
                "url": "https://doi.org/10.1038/s41589-020-0480-6",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32152544",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32152544",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-h-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2020-09-02",
        "modification_date": "2021-05-26",
        "urn": "urn:mavedb:00000046-a",
        "publish_date": "2020-09-05",
        "created_by": "0000-0001-7684-5841",
        "modified_by": "0000-0001-7684-5841",
        "extra_metadata": {},
        "abstract_text": "The membrane-associated RING-CH (MARCH) proteins are E3 ubiquitin ligases that contain transmembrane (TM) domains and regulate the cell-surface levels of key immune-stimulatory ligands such as major histocompatibility complex (MHC) molecules and the T-cell costimulatory ligand CD86. Endogenous mammalian MARCHs act on these targets to regulate antigen presentation and activation of adaptive immunity, while virus-encoded homologs target the same molecules to evade immune responses. Substrate specificity is believed to be encoded in or near the membrane-embedded domains of MARCHs and the proteins they regulate, but exactly what sequences distinguish substrates from non-substrates is poorly understood. Here we examined the requirements for recognition of the costimulatory ligand CD86 by two different MARCH-family proteins, human MARCH1 and Kaposi’s sarcoma herpesvirus (KSHV) modulator of immune recognition (MIR)2, using a deep mutational scanning (DMS) approach. We identified a highly specific recognition surface in the hydrophobic core of the CD86 TM domain that is required by MARCH1 and prominently features a proline at position 254. In contrast, MIR2 requires no specific sequences in the CD86 TM domain but relies primarily on an aspartic acid at position 244 in the CD86 extracellular juxtamembrane region. Surprisingly, while MIR2 recognized CD86 with a TM domain composed entirely of valine, many different single-amino-acid substitutions in the context of the native TM sequence conferred MIR2 resistance. These results show that the human and viral proteins evolved completely different recognition modes for the same substrate and reveal that some TM sequences may be incompatible with MIR2 activity even when no specific recognition motif is required.",
        "method_text": "The DMS library was made using overlap PCR with primers (IDT) containing NNN mixed bases and cloned into pHAGE-eF1a-MCS-IRES-ZsGreen using T4 ligase (NEB). Ligation reactions were transformed into XL1-Blue E. coli and colonies counted to ensure each position had at least 200 transformants to provide good coverage of 64 possible DNA variants.  Colonies were washed directly from LB-Agar plates into LB broth and grown until cultures were turbid (~2 hours) before plasmid DNA was recovered by miniprep (Qiagen).  1 µg of DNA from each position was combined to provide a deep mutational scanning library with complete coverage along the CD86 TM domain.  \r\n\r\nLentivirus produced from the library was titrated to result in ~10-20% transduction efficiency of 300,000 HeLa cells resulting in 30-60,000 transduced cells in each replicate.  2 days post transduction, ZsGreen positive HeLa cells were sorted from each replicate.  These cells were expanded to fill one 6-well plate well (~1 million cells) before mRNA was harvested from half of the cells (Population I), with the remainder sorted for CD86 surface expression.  CD86 positive cells were again grown to confluence before mRNA was harvested from a third of the cells (Population II), with the remainder split in two and transduced with either MARCH1 or MIR2 transducing around half of the cells as measured by mCherry expression.  Cells were expanded to confluence and sorted on mCherry expression. This population was expanded and mRNA harvested from half of the cells (Population III).  The other half was incubated with 150 ng/ml of doxycycline for 48 hours to induce MARCH1/MIR2 expression.  Cells were stained for CD86 surface expression and cells containing CD86 variants that were resistant to MARCH1 or MIR2 recovered and expanded before mRNA was harvested (Population IV).\r\n\r\nEnrichment scores of Population II versus Population I were calculated to determine cell surface levels of variant CD86 molecules.  Enrichment scores of Population IV versus Population III were used to determine which variants were poor MARCH1 or MIR2 substrates.\r\n\r\nCount Data Column Titles in CD86 Surface Expression:\r\n\r\nReplicate_x_c_0 = GFP+ Population I\r\nReplicate_x_c_1 = CD86+ Population II\r\n\r\nCount Data Column Titles in score set CD86 susceptibility to MARCH1 :\r\n\r\nReplicate_x_c_0 = CD86+ Before MARCH1 expression - Population III\r\nReplicate_x_c_1 = CD86+ After MARCH1 expression - Population IV\r\n\r\nCount Data Column Titles in score set CD86 susceptibility to MIR2:\r\n\r\nReplicate_x_c_0 = CD86+ Before MARCH1 expression - Population III\r\nReplicate_x_c_3 = CD86+ After MARCH1 expression - Population IV",
        "short_description": "A deep mutational screen of the CD86 transmembrane domain (residues 244-270) to compare the features that are recognised by the human E3 ligase MARCH1 versus the KSHV E3 ligase MIR2.",
        "title": "MARCH1 and MIR2 recognize different features of human CD86",
        "keywords": [
            {
                "text": "MIR2"
            },
            {
                "text": "CD86"
            },
            {
                "text": "DMS"
            },
            {
                "text": "mRNA"
            },
            {
                "text": "MARCH1"
            },
            {
                "text": "Flow Cytometry"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA661137",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA661137",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-7684-5841"
        ],
        "scoresets": [
            "urn:mavedb:00000046-a-1",
            "urn:mavedb:00000046-a-3",
            "urn:mavedb:00000046-a-2"
        ],
        "experimentset": "urn:mavedb:00000046"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-b",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the presence of the antibiotic to perform the selection. Two replicate selections were performed.\r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 39 μg/ml",
        "title": "TEM-1 39 μg/ml Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-b-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2021-10-28",
        "modification_date": "2021-10-28",
        "urn": "urn:mavedb:00000083-f",
        "publish_date": "2021-10-28",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis was conducted to determine the role of exonic sequences in splicing of a human RNA transcript. Minigene variants were assayed for splicing in human HEK293 cells. Ten different variant minigenes were tested, each differing by a six-nucleotide sequence at positions 5-10 in the exon. This record describes a sequence similar to an hnRNP I (PTB) binding site.",
        "method_text": "A custom synthesized 60-bp 1760,00 element microarray was purchased from Aligent. Variant minigenes were constructed using primer extension PCR. The microarray wild type clusters were present in a higher number to provide the denominator sufficient for later analysis. The 3’ end of the 60-mer was constant and the remaining 47 nucleotides were specified as wild type or variants of WT-1 exon 5. The full minigene library was constructed by three-fragment overlap extension PCR and transfected into HEK293 cells.\r\n\r\nTwo independent transfections were performed.\r\n \r\nInput DNA and reverse-transcribed RNA were amplified and prepared for sequencing. Sequencing was carried out using Illumina with 74 base pair reads.",
        "short_description": "Saturation mutagenesis for exonic base effects on splicing, similar to an hnRNP I (PTB) binding site.",
        "title": "Exonic splicing for hnRNP I (PTB) binding site",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE105785",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105785",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29242188",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29242188",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000083-f-1"
        ],
        "experimentset": "urn:mavedb:00000083"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-b",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 2, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 2 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 2 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-b-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-01-12",
        "modification_date": "2021-01-12",
        "urn": "urn:mavedb:00000055-a",
        "publish_date": "2021-01-12",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment identified candidate pharmacogenomic variants in NUDT15 that could contribute to thiopurine toxicity. Two functional assays were performed on the same variant library, one for NUDT15 activity and one for protein stability.",
        "method_text": "The NUDT15 variant library was synthesized by Twist Biosciences. The library included all possible single amino acid changes across the gene's coding region. Each variant was tagged with a random sequence barcode and the association between barcodes and variants was determined using PacBio SMRT sequencing as previously described for VAMP-seq. The barcoded library was introduced into a HEK293T landing pad cell line.\r\n\r\nCells expressing NUDT15 variants fused to EGFP were sorted into 4 bins based on EGFP signal normalized to mCherry by FACS. Genomic DNA was extracted from each bin and barcodes were sequenced on an Illumina HiSeq 2000 to obtain binwise variant-barcode counts. An unspecified number of replicates were performed.",
        "short_description": "NUDT15 protein stability measured by VAMP-seq.",
        "title": "NUDT15 protein stability assay",
        "keywords": [
            {
                "text": "VAMP-seq"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "32094176",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32094176",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000055-a-1"
        ],
        "experimentset": "urn:mavedb:00000055"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-09-16",
        "urn": "urn:mavedb:00000068-c",
        "publish_date": "2021-09-16",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors leveraged CRISPR-Cas9 technique to construct cell lines without wild type TP53 expression (p53NULL) in A549 human lung carcinoma. These cell lines are later transferred with p53 mutant library in order to study the function of these variants. This study used etoposide which induces DNA double-strand break during the selection process. This paper was using an older version of TP53 reference sequence, and we are depositing the result according to the latest reference sequence.",
        "method_text": "This study used Mutagenesis by Integrated TilEs (MITE) method to generate the TP53 variant library which includes all single position missense and nonsense mutations as well as synonymous mutants. The p53Null cell line is infected with this library and cultured with etoposide for 12 days. Variant frequency before and after selection are determined by Hiseq4000.",
        "short_description": "TP53 saturation mutagenesis screens with TP53 null cell line using etoposide which is a DNA double-strand break-inducing agent.",
        "title": "Mutated p53 with etoposide",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1038/s41588-018-0204-y",
                "url": "https://doi.org/10.1038/s41588-018-0204-y",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "30224644",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30224644",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000068-c-1"
        ],
        "experimentset": "urn:mavedb:00000068"
    },
    {
        "creation_date": "2020-06-29",
        "modification_date": "2020-06-29",
        "urn": "urn:mavedb:00000045-g",
        "publish_date": "2020-06-29",
        "created_by": "0000-0002-2020-2641",
        "modified_by": "0000-0002-2020-2641",
        "extra_metadata": {},
        "abstract_text": "alpha-Synuclein is a conformationally dynamic protein linked to a variety of neurodegenerative diseases, including Parkinson’s. Conformational transitions of this protein are believed to contribute to disease etiology, but the conformations that drive pathology remain unclear. To address this question, we screened an exhaustive library of alpha-synuclein missense variants for their toxicity in yeast, a well-validated cellular model for alpha-synuclein pathobiology. By examining the pattern of mutations that disrupts cellular toxicity, we were able to build a model for the structure of the toxic species.",
        "method_text": "A double-stranded DNA library based on human alpha-synuclein cDNA was produced by commercial oligonucleotide synthesis and assembly. The designed library encodes all single missense variants of alpha-synuclein, each encoded by a single codon. This library was cloned in frame with a C-terminal GFP fusion, and 26bp random barcodes were appended 3’ to the stop codon to facilitate repeated selection. This construct was cloned under control of an inducible promoter and transformed into E. coli. Following restrictive transformation, the final library diversity was ~60,000 unique clones, corresponding to ~20 barcodes per missense variant. The barcoded coding region was amplified and analyzed by long-read MiSeq in order to associate barcodes with coding sequences. The resulting lookup table expedites subsequent quantification of variant frequencies.\r\nThis plasmid library was then transformed into yeast. Selection was performed by inducing expression and collecting aliquots over time. Additional experiments were performed in yeast treated with small molecules. Finally, the expression level of each variant was estimated by cell sorting yeast cells based on the fluorescence of the GFP fusion.",
        "short_description": "The toxicity of alpha-synuclein missense variants was determined by measuring their change in frequency during yeast outgrowth",
        "title": "Deep Mutational Scanning of alpha-Synuclein based on Toxicity in Yeast Treated with Dopamine",
        "keywords": [
            {
                "text": "alpha-synuclein"
            },
            {
                "text": "protein folding"
            },
            {
                "text": "yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA564806",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA564806",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.05.01.072884",
                "url": "https://doi.org/10.1101/2020.05.01.072884",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-2020-2641"
        ],
        "scoresets": [
            "urn:mavedb:00000045-g-1"
        ],
        "experimentset": "urn:mavedb:00000045"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000034-b",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of ZRS enhancer in NIH3T3 cells. Co-transfected with Hoxd13 and Hand2.",
        "title": "Saturation mutagenesis MPRA of ZRS enhancer, Hoxd13+Hand2",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444737",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444737",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444909",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444909",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444910",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444910",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444911",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444911",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444810",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444810",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444811",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444811",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "SRX5444812",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444812",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000034-b-1"
        ],
        "experimentset": "urn:mavedb:00000034"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-j",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 15, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 15 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 15 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-j-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-07-08",
        "modification_date": "2022-06-08",
        "urn": "urn:mavedb:00000095-a",
        "publish_date": "2022-06-08",
        "created_by": "0000-0002-0730-2576",
        "modified_by": "0000-0002-0730-2576",
        "extra_metadata": {},
        "abstract_text": "This study measured the functional consequences of mutations in CYP2C9, as measured by two different assays, one using Variant Abundance by Massively Parallel sequencing (VAMP-seq) in HEK293T cells, and one using a yeast activity-based protein profiling assay (Click-seq).\r\n\r\nThis entry contains amino acid scores from the activity assay in humanized yeast cells.",
        "method_text": "CYP2C9 variant libraries were generated using inverse PCR with NNK primers. Variants were tagged with 18bp random sequence barcodes and the association between barcodes and variants was determined using PacBio sequencing. The barcoded activity library was introduced into a humanized yeast strain. \r\n\r\nCells expressing CYP2C9 variants were sorted into 4 bins by FACS. Plasmid DNA was extracted and barcodes from each bin were sequenced. Four replicate sorts were performed. Barcodes from each bin were counted and associated with variant sequences using Enrich2. Variant activity scores were calculated from the weighed average of variant frequencies in each bin, such that high activity variants have a higher score and low activity variants have a lower score. Activity scores were normalized to the median synonymous variant score (set to 1) and the median nonsense variant score (set to 0). Confidence intervals and variance estimates are based on replicate scores.",
        "short_description": "CYP2C9 activity measured by a yeast activity-based protein profiling assay (Click-seq)",
        "title": "CYP2C9 activity scores",
        "keywords": [
            {
                "text": "NNK mutagenesis"
            },
            {
                "text": "FACS"
            },
            {
                "text": "humanized yeast"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE165412",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165412",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "34314704",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/34314704",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "29785012",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29785012",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0002-0730-2576"
        ],
        "scoresets": [
            "urn:mavedb:00000095-a-1"
        ],
        "experimentset": "urn:mavedb:00000095"
    },
    {
        "creation_date": "2020-08-23",
        "modification_date": "2020-12-10",
        "urn": "urn:mavedb:00000052-a",
        "publish_date": "2020-12-10",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study generated thousands of mutated sequence on Gcn4 activation domain which contains one or several amino acid substitutions. They used a high-throughput fluorescent reporter assay to identify the transcription ability of mutated Gcn4 sequences through cell sorting.",
        "method_text": "The designed mutated Gcn4 activation domain was combined to a synthetic transcription factor and expressed in yeast. The transcription factor is tailed with mCherry and functioning transcription factor is able to facilitate the expression of GFP which is the genome-integrated reporter gene. Cells with distinct Gcn4 activity are sorted by fluorescence-activated cell sorting system to several bins according to the ratio of GFP and mCherry fluorescence. The cells are sorted into 8 bins: bin 1 with low GFP or mCherry level; bin 2 with low GFP level and normal mCherry level; and the other bins are evenly partitioned according to the ratio of the two fluorscence. The variant abundance is determined by high-throughput sequencing in an Illumina platform. This process is repeated one more time.",
        "short_description": "Mutagenesis study of Gcn4 activation domain in complete media using fluorescent reporter assay.",
        "title": "Gcn4 activation domain activity",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.17632/rbfr6m4733.1",
                "url": "https://doi.org/10.17632/rbfr6m4733.1",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "29525204",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29525204",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000052-a-1"
        ],
        "experimentset": "urn:mavedb:00000052"
    },
    {
        "creation_date": "2021-09-29",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-f",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 4 µg/mL cefotaxime at 37C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 4 µg/mL cefotaxime at 37C",
        "title": "VIM-2 4 µg/mL CTX at 37C",
        "keywords": [
            {
                "text": "cefotaxime"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-f-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000092-a",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors use a deep mutational scan to characterize the fitness landscape of Influenza A virus (A/WSN/1933(H1N1)) hemagglutinin, e.g. determining how all possible single mutations impact the ability of influenza to replicate in human cells. Mutant viruses were selected for replication in human MDCK-SIAT1 cells across serial dilutions.",
        "method_text": "The authors use a deep mutational scan to characterize the fitness landscape of Influenza A virus (A/WSN/1933(H1N1)) hemagglutinin, e.g. determining how all possible single mutations (over full length = 565aa) impact the ability of influenza to replicate in human cells. A mutant library of hemaglutinin was transformed into viruses and allowed to replicate in human MDCK-SIAT1 cells across serial dilutions. Mutants that negatively affect viral replication have low copy numbers in the final sequenced library, and receive low scores. The library was generated by low-cycle PCR with NNN codons.",
        "short_description": "Deep mutational scan of Influenza A virus (A/WSN/1933(H1N1)) Hemagglutinin selecting for viral replication in human cells.",
        "title": "Influenza HA viral replication",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "SRP040983",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP040983",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25006036",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25006036",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000092-a-1"
        ],
        "experimentset": "urn:mavedb:00000092"
    },
    {
        "creation_date": "2021-03-14",
        "modification_date": "2021-04-15",
        "urn": "urn:mavedb:00000063-b",
        "publish_date": "2021-04-15",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the variant effects of <i>E.coli</i> dihydrofolate reductase (DHFR) whose function is necessary for the survival of bacteria. The study cultured the bacteria in an early Log phase growth period without the control of Lon protease and determined the variant frequency change after cultivation, indicating the impact of DHFR variants.",
        "method_text": "The variant library in this study is generated by parallel inverse PCR reactions. An <i>E.coli</i> strain with deficient Lon gene is introduced with the variant library and cultivated. The growth rates of the bacteria harbouring each variant at several timepoints are determined by Illumina NextSeq, and the results are analyzed by Enrich2. The experiments are repeated three times in total and the final fitness values are the average of them.",
        "short_description": "Growth rate of E.coli with mutated dihydrofolate reductase (DHFR) with deficient Lon protease",
        "title": "Growth rate of mutated DHFR with deficient Lon",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA590072",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA590072",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.7554/eLife.53476",
                "url": "https://doi.org/10.7554/eLife.53476",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "32701056",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32701056",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000063-b-1"
        ],
        "experimentset": "urn:mavedb:00000063"
    },
    {
        "creation_date": "2019-08-08",
        "modification_date": "2019-08-08",
        "urn": "urn:mavedb:00000042-a",
        "publish_date": "2019-08-08",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This is a dataset demonstrating the use of landing pad cell lines to generate recombinant mammalian cells. The experiment measured the effect of mutating the start codon of an EGFP construct with an N-terminal ubiquitin fusion. Once the ubiquitin is removed by cellular DUBs, the protein exposes a new N-terminal amino acid, which may target the protein for degradation.",
        "method_text": "Plasmids with an NNN N-terminal codon were created and introduced into HEK293T cells. Cells were sorted into four equally sized bins based on fluorescence and the genomic DNA containing the NNN codon was sequenced using Illumina amplicon sequencing.",
        "short_description": "Mutagenesis of the start codon of EGFP and its effect on an N-terminal fusion.",
        "title": "EGFP N-terminal codon",
        "keywords": [
            {
                "text": "NNN mutagenesis"
            },
            {
                "text": "FACS"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP095490",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP095490",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28335006",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28335006",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000042-a-1"
        ],
        "experimentset": "urn:mavedb:00000042"
    },
    {
        "creation_date": "2019-02-17",
        "modification_date": "2019-07-28",
        "urn": "urn:mavedb:00000009-a",
        "publish_date": "2019-02-18",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the impact of nearly all possible point mutations in the *SUL1* promoter, which is frequently amplified under sulfate-limited growth conditions. The results demonstrated that the optimal set of observed point mutations were able to increase organismal fitness by 11%, which is far below the fitness increases previously measured for amplification of *SUL1* (35% or higher). These experiments also revealed the fitness effects of creating new transcription factor binding sites in the existing promoter sequence.",
        "method_text": "Variants were generated using error-prone PCR and linked to 12-base DNA barcodes. The relationship between barcode and variant sequence was determined using subassembly [Hiatt et al.]. Yeast strains with genomic SUl1 deletions were transformed with a centromeric plasmid containing SUL1 with a barcoded variant promoter. Cells were cultured in sulfate- or glucose- limited conditions using chemostats.",
        "short_description": "Comprehensive analysis of the SUL1 promoter of Saccharomyces cerevisiae under glucose and sulfate limited growth.",
        "title": "Comprehensive analysis of the SUL1 promoter",
        "keywords": [
            {
                "text": "subassembly"
            },
            {
                "text": "error-prone PCR"
            },
            {
                "text": "promoter"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA273419",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA273419",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "20081835",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/20081835",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "26936925",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26936925",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000009-a-2",
            "urn:mavedb:00000009-a-1"
        ],
        "experimentset": "urn:mavedb:00000009"
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000078-a",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study tested the carboxylation activity change of vitamin K epoxide reductase (VKOR) variants. The functioning VKOR is able to carboxylate Factor IX domain which is secreted and retained on the cell surface. By culturing the cells with fluorophore-labeled carboxylation-specific antibody, the impact of VKOR variants to its carboxylation activity can be determined by FACS.",
        "method_text": "The variant library is generated by mutagenesis primers through PCR which contains 697 missense mutations. The cell line is binded with a fluorophore-labeled carboxylation-specific antibody and sorted into quartile bins according to the APC fluorescent intensity by FACS. Each bin is deeply sequenced and the final abundance scores are calculated.",
        "short_description": "Carboxylation activity of VKOR variants by substrate surface expression.",
        "title": "VKOR carboxylation activity",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "GSE149922",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149922",
                "dbversion": null,
                "dbname": "SRA"
            },
            {
                "identifier": "PRJNA630502",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA630502",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32870157",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32870157",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000078-a-1"
        ],
        "experimentset": "urn:mavedb:00000078"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-a",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 2, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 2 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 2 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-a-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-r",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 19, replicate 2. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 19 replicate 2 pre-normalization scores",
        "title": "BRCA1 SGE Exon 19 Replicate 2",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-r-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-10-02",
        "modification_date": "2021-10-02",
        "urn": "urn:mavedb:00000080-a",
        "publish_date": "2021-10-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured fluorescence levels of mutants of the Aequorea victoria GFP (avGFP) using error-prone PCR, FACS, and a probability model developed using the observed fluorescence levels. Epistasis of mutations was also discussed, using a model of sequence divergence.",
        "method_text": "The starting sequence was designed to contain mutation F64L to enhance folding in E. coli at 37°C and optimized codons. Starting from this sequence, a variant library was generated using error-prone PCR and primers that introduced barcodes downstream of the GFP coding sequence. The avGFP variants were fused to mKate2, a red fluorescent protein, with a rigid alpha-helical linker to assure accurate measurements of green fluorescence that are independent of the variance in the protein expression levels. The fusion library was inserted into pQE-30 expression vectors and used to transform E. coli XL1 Blue.\r\n\r\nCells were sorted into eight bins using FACS Aria III cell sorter (BD Biosciences). Barcodes in each of the eight populations were sequenced using Illumina HiSeq for fluorescence estimation.",
        "short_description": "Deep mutational scan evaluating the effect of mutations on fluorescence of Aequorea victoria GFP.",
        "title": "GFP mutations and fluorescence levels",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "PRJNA282342",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA282342",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.6084/m9.figshare.3102154",
                "url": "http://doi.org/10.6084/m9.figshare.3102154",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27193686",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27193686",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2072-3436"
        ],
        "scoresets": [
            "urn:mavedb:00000080-a-1",
            "urn:mavedb:00000080-a-2"
        ],
        "experimentset": "urn:mavedb:00000080"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-c",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the presence of the antibiotic to perform the selection. Two replicate selections were performed.\r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 156 μg/ml",
        "title": "TEM-1 156 μg/ml Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-c-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-01-17",
        "urn": "urn:mavedb:00000057-b",
        "publish_date": "2021-01-17",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors used saturation mutagenesis to study the variant effect of Ras, with the regulation of GTPase activating protein (GAP) but in the absence of guanine nucleotide exchange factor (GEF). The variants were selected by bacterial two-hybrid strategy.",
        "method_text": "The RAS mutant library was generated by oligonucleotide-directed mutagenesis. The mutant library was transfected into bacteria without GEF expression and the functioning RAS protein which will bind to GTP as well as Raf. The binding of these molecules can trigger the transcription of an antibiotic resistant factor. The library was separated to three sub-libraries in order to cover the whole RAS gene length which ranges from the residue 2-56, 57-111, and 112-166. These samples were selected individually. The samples in different sub-libraries were barcoded and pooled together for MiSeq sequencing.",
        "short_description": "Selection result of Ras mutants expressed in the presence of the GAP, but without the GEF",
        "title": "Attenuated-Ras",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28686159",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28686159",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000057-b-1"
        ],
        "experimentset": "urn:mavedb:00000057"
    },
    {
        "creation_date": "2021-10-01",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000077-a",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study determined the effect of amino acid substitutions on cohesin-dockerin binding using deep mutational scanning. Cohesins from *Clostridium thermocellum* and *Clostridium cellulolyticum* were analyzed using yeast display.",
        "method_text": "Single site mutagenesis was performed using NNN PCR (Pfunkel) to create a site saturation mutagenesis library. *C. cellulolyticum* cohesin was segmented into two tiles and sequenced using 250-bp paired-end reads.\r\n\r\nCohesin mutants were displayed on the surface of yeast and incubated with biotinylated dockerin. A C-terminal c-myc tag on the cohesin domain was used to measure protein expression and streptavidin-conjugated fluorophores were used to measure binding. Cells in the top 5% by fluorescence were used as the “selected” population for score calculation.",
        "short_description": "Deep mutational scan of C. cellulolyticum cohesin binding affinity for dockerin.",
        "title": "C. cellulolyticum cohesin binding affinity",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "27699856",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27699856",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "scoresets": [
            "urn:mavedb:00000077-a-2",
            "urn:mavedb:00000077-a-1"
        ],
        "experimentset": "urn:mavedb:00000077"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-q",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 19, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 19 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 19 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-q-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-09-29",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-h",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 0.031 µg/mL meropenem at 37C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 0.031 µg/mL meropenem at 37C",
        "title": "VIM-2 0.031 µg/mL MEM at 37C",
        "keywords": [
            {
                "text": "antibiotic resistance"
            },
            {
                "text": "meropenem"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-h-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2019-07-29",
        "modification_date": "2019-07-29",
        "urn": "urn:mavedb:00000037-a",
        "publish_date": "2019-07-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study performed a bulk growth competition experiment measuring the effect of point mutations on ubiquitin structure and function. The results were consistent with previous studies of individual mutants as well as Alanine-scanning. Positions were clustered by their tolerance of mutations and highly sensitive regions were mapped.",
        "method_text": "Variant construction, DNA sequencing, and analysis was conducted using EMPIRIC [Hietpas et al.]. Variants were transformed into the Sub328 ubiquitin shutoff strain, which produces sufficient ubiquitin in galactose but not in dextrose. The competition assay was therefore performed in dextrose media, whereas the libraries were constructed and maintained in galactose media.",
        "short_description": "Deep mutational scan of ubiquitin in a yeast growth assay",
        "title": "Ubiquitin yeast growth",
        "keywords": [
            {
                "text": "EMPIRIC"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "ubiquitin"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "21464309",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/21464309",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23376099",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23376099",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000037-a-1"
        ],
        "experimentset": "urn:mavedb:00000037"
    },
    {
        "creation_date": "2021-11-02",
        "modification_date": "2021-11-02",
        "urn": "urn:mavedb:00000085-c",
        "publish_date": "2021-11-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 β-lactamase gene in *Escherichia coli* on different backgrounds. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "The variant library was constructed using PFunkel comprehensive codon mutagenesis. One NNN-containing mutagenic primer was used per codon.\r\n\r\nThis dataset describes variants on the TEM-15 background, which differs from TEM-1 by p.[Glu102Lys;Gly236Ser] (TEM-1 position not Ambler position).\r\n\r\nThe band-pass selection system is described in (Sohka et al., 2009). Briefly, cells are plated on media containing Tet and a variable concentration of Amp. If TEM-1 activity is too low for the Amp concentration, cells will not proliferate. If TEM-1 activity is too high, no cell wall damage will occur and TetC (which confers Tet resistance) will not be produced. Therefore cells should only grow if the TEM-1 variant’s activity level matches the Amp concentration.\r\n\r\nSequencing was performed using PacBio.",
        "short_description": "TEM-15 (TEM-1 variant) fitness on Amp.",
        "title": "TEM-15 Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "27173379",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27173379",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000085-c-1"
        ],
        "experimentset": "urn:mavedb:00000085"
    },
    {
        "creation_date": "2021-09-28",
        "modification_date": "2021-09-29",
        "urn": "urn:mavedb:00000073-a",
        "publish_date": "2021-09-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Saturation mutagenesis of VIM-2 metallo-β-lactamase was performed to determine substrate recognition and better understand the ability to recognize new substrates. The VIM-2 signal peptide plays a role in expression and transport and was included in the analysis. Relative fitness was determined in the presence of three antibiotics (ampicillin, cefotaxime, and meropenem).",
        "method_text": "The variant library was constructed using degenerate NNN codons introduced by PCR to generate libraries of single amino acid mutations. Seven libraries were constructed, each with 39 consecutive codons (33 for the last library) to enable fully-overlapping 150-bp paired-end sequencing using Illumina NextSeq.\r\n\r\nTwo replicate selections were performed for each library.\r\n\r\nAn additional GGA (Gly) codon was introduced immediately after the start codon in order to create an NcoI restriction site for cloning into the pIDR2 (chloramphenicol resistance) plasmid.\r\n\r\nThe variant library was transformed into E.coli (E. cloni 10G strain) and selected for chloramphenicol resistance. These cells containing the VIM-2 plasmid were then split into 7 different groups for antibiotic selection.\r\n\r\nThis record describes the selection performed on VIM-2 at 128 µg/mL ampicillin at 25C.",
        "short_description": "Deep mutational scan of VIM-2 metallo-β-lactamase at 128 µg/mL ampicillin at 25C",
        "title": "VIM-2 128 µg/mL AMP at 25C",
        "keywords": [
            {
                "text": "ampicillin"
            },
            {
                "text": "antibiotic resistance"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA606894",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA606894",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32510322",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32510322",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000073-a-1"
        ],
        "experimentset": "urn:mavedb:00000073"
    },
    {
        "creation_date": "2021-11-13",
        "modification_date": "2021-11-13",
        "urn": "urn:mavedb:00000089-a",
        "publish_date": "2021-11-13",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "A mutation scan was performed to discover the mutants and sites responsible for Influenza sensitivity to the innate-immune restriction factor MxA.",
        "method_text": "Experiments made use of an existing Influenza (H3N2, Aichi/1968) nucleoprotein mutant library, created previously via NNN PCR (see Doud *et al.*).  Viruses were constructed by co-transfecting the mutant nucleoprotein library plus the remaining influenza genes into human MDCK-SIAT1 cells. Selection was performed by replication and serial dilution in MDCK-SIAT1 cells constitutively expressing human MxA. As a negative control for normalization, selection was likewise performed but with MDCK-SIAT1 cells expressing mutant, inactive MxA. Variants receive high scores when relatively higher enrichment in the active MxA is measured versus enrichment under inactive MxA.",
        "short_description": "Deep mutational scan of Influenza (H3N2, Aichi/1968) nucleoprotein for resistance to MxA.",
        "title": "Influenza nucleoprotein resistance to human MxA",
        "keywords": [
            {
                "text": "Influenza"
            },
            {
                "text": "Viral replication"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRP082554",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP082554",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28346537",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28346537",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "26226986",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/26226986",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000089-a-1"
        ],
        "experimentset": "urn:mavedb:00000089"
    },
    {
        "creation_date": "2022-08-25",
        "modification_date": "2022-08-26",
        "urn": "urn:mavedb:00000103-b",
        "publish_date": "2022-08-26",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "Characterization of function and ERK-inhibitor sensitivity of 6,810 ERK2 mutants. \r\nA pooled, virally delivered, doxycycline-induced, cDNA expression library containing all 19 amino acid substitutions at residues 2–360 of ERK2 generated with Mutagenesis by Integrated TilEs (MITE) and transduced into BRAFV600E mutatant A375 cells. Selected in a pooled competition assay, where LOF ERK2 mutants are enriched relative to those with wild-type activity and GOF mutants depleted.\r\nScore is an average of 4 replicates normalized to the total reads per lane and log2 transformed\r\n\r\nInduced with DOX",
        "short_description": "Phenotypic Characterization of a Comprehensive Set of 6,810 MAPK1/ERK2 Missense Mutants\r\nDOX induced time point that enriches for LOF mutants and depletes GOF mutants",
        "title": "MAPK1 DOX Induced",
        "keywords": [
            {
                "text": "resistance"
            },
            {
                "text": "complementation"
            },
            {
                "text": "MAPK1"
            },
            {
                "text": "ERK2"
            },
            {
                "text": "MITE"
            },
            {
                "text": "VRT-11E"
            },
            {
                "text": "SCH772984"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1016/j.celrep.2016.09.061",
                "url": "http://doi.org/10.1016/j.celrep.2016.09.061",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "27760319",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27760319",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "scoresets": [
            "urn:mavedb:00000103-b-1"
        ],
        "experimentset": "urn:mavedb:00000103"
    },
    {
        "creation_date": "2019-01-23",
        "modification_date": "2019-07-26",
        "urn": "urn:mavedb:00000007-a",
        "publish_date": "2019-01-24",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study described the functional consequence of over 100,000 enhancer variants *in vivo* in mouse liver. Two human enhancers (ALDOB, ECR11) and one mouse enhancer (LTV1) were known to be active in mouse liver and therefore variants in these enhancers should show a measurable difference in transcription. The results were broadly consistent with evolutionary data and transcription factor binding sites, but were not always concordant demonstrating the importance of measuring the effect of enhancer variants directly.\r\n\r\nThis MaveDB entry describes the ECR11 enhancer data. Datasets for other enhancers described in the same publication are also available: [ALDOB](https://www.mavedb.org/experiment/urn:mavedb:00000006-a/) [LTV1](https://www.mavedb.org/experiment/urn:mavedb:00000008-a/)",
        "method_text": "Variants were constructed using doped oligo with 1% of each non-target base included at each position (ratio of 97:1:1:1). Full-length enhancer haplotypes were assembled and cloned into tagged pGL4.23 plasmids. Each variant haplotype was tagged with a 20-bp sequence, with one tag per haplotype in almost all cases. Each single nucleotide change was present in at least 42 haplotypes. \r\n\r\nThe enhancers were injected into the mouse tail vein and mouse livers were harvested after 24h. RNA was isolated from fresh mouse livers, subjected to DNAseI treatment to remove any DNA contamination, reverse-transcribed into cDNA, and sequenced.\r\n\r\nTwo sets of sequencing reactions were performed. One used short Illumina reads (42 total cycles) to sequence the tag sequence used for quantifying each enhancer's activity. The other used subassembly synthetic long read sequencing to associate the tags with the full-length enhancer haplotypes.",
        "short_description": "Massively parallel functional dissection of the ECR11 enhancer in a mouse liver transcription assay.",
        "title": "Massively parallel functional dissection of ECR11 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "doped oligo synthesis"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "liver"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRA049159",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRA049159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "22371081",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/22371081",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000007-a-1"
        ],
        "experimentset": "urn:mavedb:00000007"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-e",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 10h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 10h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-e-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2021-08-16",
        "modification_date": "2021-08-16",
        "urn": "urn:mavedb:00000067-a",
        "publish_date": "2021-08-16",
        "created_by": "0000-0001-6465-5776",
        "modified_by": "0000-0001-6465-5776",
        "extra_metadata": {},
        "abstract_text": "TECR variant effect map (Abstract - to be updated)",
        "method_text": "TECR variant effect map (Method - to be updated)",
        "short_description": "TECR variant effect map (Short description - to be updated)",
        "title": "TECR variant effect map",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0001-6465-5776"
        ],
        "scoresets": [
            "urn:mavedb:00000067-a-1"
        ],
        "experimentset": "urn:mavedb:00000067"
    },
    {
        "creation_date": "2021-10-01",
        "modification_date": "2022-08-16",
        "urn": "urn:mavedb:00000077-b",
        "publish_date": "2022-08-16",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study determined the effect of amino acid substitutions on cohesin-dockerin binding using deep mutational scanning. Cohesins from *Clostridium thermocellum* and *Clostridium cellulolyticum* were analyzed using yeast display.",
        "method_text": "Single site mutagenesis was performed using NNN PCR (Pfunkel) to create a site saturation mutagenesis library. *C. thermocellum* cohesin was segmented into four tiles and sequenced using 150-bp paired-end reads.\r\n\r\nCohesin mutants were displayed on the surface of yeast and incubated with biotinylated dockerin. A C-terminal c-myc tag on the cohesin domain was used to measure protein expression and streptavidin-conjugated fluorophores were used to measure binding. Cells in the top 5% by fluorescence were used as the “selected” population for score calculation.",
        "short_description": "Deep mutational scan of C. thermocellum cohesin binding affinity for dockerin.",
        "title": "C. thermocellum cohesin binding affinity",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "27699856",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27699856",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-3537-3865"
        ],
        "scoresets": [
            "urn:mavedb:00000077-b-2",
            "urn:mavedb:00000077-b-1"
        ],
        "experimentset": "urn:mavedb:00000077"
    },
    {
        "creation_date": "2021-11-02",
        "modification_date": "2021-11-02",
        "urn": "urn:mavedb:00000085-b",
        "publish_date": "2021-11-02",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment measured the experimental fitness of variants in the TEM-1 β-lactamase gene in *Escherichia coli* on different backgrounds. Fitness measurements were estimated based on growth under increasing concentrations of ampicillin using a band-pass selection system.",
        "method_text": "The variant library was constructed using PFunkel comprehensive codon mutagenesis. One NNN-containing mutagenic primer was used per codon.\r\n\r\nThis dataset describes variants on the TEM-17 background, which differs from TEM-1 by p.Glu102Lys (TEM-1 position not Ambler position).\r\n\r\nThe band-pass selection system is described in (Sohka et al., 2009). Briefly, cells are plated on media containing Tet and a variable concentration of Amp. If TEM-1 activity is too low for the Amp concentration, cells will not proliferate. If TEM-1 activity is too high, no cell wall damage will occur and TetC (which confers Tet resistance) will not be produced. Therefore cells should only grow if the TEM-1 variant’s activity level matches the Amp concentration.\r\n\r\nSequencing was performed using PacBio.",
        "short_description": "TEM-17 (TEM-1 variant) fitness on Amp.",
        "title": "TEM-17 Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "23284860",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23284860",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "24567513",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24567513",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "19502423",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/19502423",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "27173379",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/27173379",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000085-b-1"
        ],
        "experimentset": "urn:mavedb:00000085"
    },
    {
        "creation_date": "2022-08-31",
        "modification_date": "2022-09-05",
        "urn": "urn:mavedb:00000104-a",
        "publish_date": "2022-09-05",
        "created_by": "0000-0001-6624-4698",
        "modified_by": "0000-0001-6624-4698",
        "extra_metadata": {},
        "abstract_text": "",
        "method_text": "A dense CRISPR library comprising 489 guides targeting PARP1 was synthesised (Twist Biosciences, Supplementary Data 4) and cloned into the BbsI site of pKLV5-U6gRNA5-PGKPuroBFP27. One million cells from each of two SUM149 PARP1-tagGFP2 clones were infected at MOI 0.3 as above and selected in puromycin. Cas9 was induced by treatment with doxycycline for 2 days after which cells were replated and 100 nM talazoparib added.\r\nOne microgram of total RNA was converted to cDNA with SuperScript III (ThermoFisher) and a GFP-specific primer (5′-CCTTGATGCCGTTCTTCTGCTTG-3′), which allowed for amplification only of the target PARP1-GFP transcripts. The GFP-positive talazoparib resistant population was enriched by cell sorting (BD FACSAria).\r\nPurified RT-PCR products were mixed and sequenced using the Ion Torrent PGM and a 318 chip with 850 flows. Data were converted to FASTQ format and aligned to the PARP1 cDNA sequence (ENST00000366794) using Novoalign (Novocraft technologies). Mutations were called from the alignments using the Ensembl Variant Effect Predictor REST API54 (implementation: github.com/GeneFunctionTeam/bioruby-sam-mutation). Coverage was calculated per base using samtools pileup (github.com/samtools, v1.5) with a maximum depth of 300,000.",
        "short_description": "high-density CRISPR-Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance",
        "title": "PARP1 dense CRISPR",
        "keywords": [
            {
                "text": "PARP1"
            },
            {
                "text": "GFP"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJEB24332",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJEB24332",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-018-03917-2",
                "url": "http://doi.org/10.1038/s41467-018-03917-2",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "29748565",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29748565",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0001-6624-4698"
        ],
        "scoresets": [
            "urn:mavedb:00000104-a-1",
            "urn:mavedb:00000104-a-2"
        ],
        "experimentset": "urn:mavedb:00000104"
    },
    {
        "creation_date": "2021-01-12",
        "modification_date": "2021-01-12",
        "urn": "urn:mavedb:00000055-b",
        "publish_date": "2021-01-12",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment identified candidate pharmacogenomic variants in NUDT15 that could contribute to thiopurine toxicity. Two functional assays were performed on the same variant library, one for NUDT15 activity and one for protein stability.",
        "method_text": "The NUDT15 variant library was synthesized by Twist Biosciences. The library included all possible single amino acid changes across the gene's coding region. Each variant was tagged with a random sequence barcode and the association between barcodes and variants was determined using PacBio SMRT sequencing as previously described for VAMP-seq. The barcoded library was introduced into a HEK293T landing pad cell line.\r\nThiopurine cytotoxicity was measured by comparing cells that were treated with 3$\\mu$m 6-thioguanine or culture media for 6 days. After treatment, genomic DNA was extracted and barcodes were sequenced on an Illumina HiSeq 2000 to obtain variant-barcode counts. Each drug treatment had 4 replicates.",
        "short_description": "NUDT15 activity scores measured by a thiopurine-cytotoxicity-based screen.",
        "title": "NUDT15 activity scores",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "32094176",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/32094176",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000055-b-1"
        ],
        "experimentset": "urn:mavedb:00000055"
    },
    {
        "creation_date": "2020-10-15",
        "modification_date": "2020-11-25",
        "urn": "urn:mavedb:00000050-a",
        "publish_date": "2020-11-25",
        "created_by": "0000-0002-6145-882X",
        "modified_by": "0000-0002-6145-882X",
        "extra_metadata": {},
        "abstract_text": "In this study a massively parallel screen was performed in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2.",
        "method_text": "Massively parallel single codon mutagenesis was used to generate comprehensive libraries of MSH2 cDNA variants. The resulting libraries were cloned into inducible lentiviruses and used to transduce HAP1 MSH2-null cells at an MOI < 1 (one integrated copy/cell).  MSH2 functional complementation was tested by inducing the stably integrated MSH2 variants and selecting with the compound 6-TG which is selectively toxic to MMR deficient cells.  Deep amplicon sequencing was used to quantify enriched LOF alleles of MSH2 in the 6-TG selected condition relative to the starting population and to mock conditions.",
        "short_description": "Massively parallel functional testing of MSH2 missense variants conferring Lynch Syndrome risk",
        "title": "MSH2 deep mutational scan",
        "keywords": [
            {
                "text": "MSH2"
            },
            {
                "text": "deep mutational scanning"
            },
            {
                "text": "Lynch Syndrome"
            }
        ],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1101/2020.06.03.133017",
                "url": "https://doi.org/10.1101/2020.06.03.133017",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [],
        "contributors": [
            "0000-0002-6145-882X"
        ],
        "scoresets": [
            "urn:mavedb:00000050-a-1"
        ],
        "experimentset": "urn:mavedb:00000050"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-c",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 3, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 3 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 3 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-c-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2021-09-20",
        "modification_date": "2021-09-20",
        "urn": "urn:mavedb:00000071-a",
        "publish_date": "2021-09-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "Deep mutational scanning was used on a library of 1.9x10^7 *Streptococcus pyogenes* Cas9 (SpCas9) variants to infer the effects of each mutation and screen for functional changes. A selection system in *E. coli* was established to differentiate between active and inactive mutant variants of SpCas9. The biological system used positive and negative selection to assay SpCas9 nuclease function in order to gather information about amino acids that allow SpCas9 to cleave DNA.",
        "method_text": "Positive selection plasmids pACYC184-tacP-ccdB-T2 were used to perform selection of SpCas9 variants by generating electrocompetent cells. These cells were electroporated and plated on both selection and control plates. The SpCas9 mutant library was cloned and extrapolated to be transformed into positive and negative selection competent cells. Following recovery, the transformations were used to perform titrations for negative selection, positive selection, and controls. Specific mutant cloning was performed by generating overlapping fragments necessary to produce chosen mutation combinations. Following that, the cells were pooled together and analyzed using Flow cytometry on a Becton Dickinson FACSAria. Next generation sequencing was performed using an Illuman NextSeq using 2x150bp paired-end reads.",
        "short_description": "Positive (on-target) selection of SpCas9 in a bacterial selection system.",
        "title": "SpCas9 positive selection",
        "keywords": [],
        "sra_ids": [
            {
                "identifier": "SRP107783",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRP107783",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "29203891",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/29203891",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000071-a-1"
        ],
        "experimentset": "urn:mavedb:00000071"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000021-a",
        "publish_date": "2019-02-19",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of IRF4 enhancer in SK-MEL-28 cells.",
        "title": "Saturation mutagenesis MPRA of IRF4 enhancer",
        "keywords": [
            {
                "text": "IRF4"
            },
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444721",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444721",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000021-a-1"
        ],
        "experimentset": "urn:mavedb:00000021"
    },
    {
        "creation_date": "2019-08-08",
        "modification_date": "2019-08-09",
        "urn": "urn:mavedb:00000041-b",
        "publish_date": "2019-08-08",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study infers the activity of variants in Src kinases's SH4 domain by measuring their effects on yeast growth, and therefore phosphotransferase activity. The resulting dataset includes variants classified as gain of function, loss of function. or neutral.",
        "method_text": "Variants in the Src SH4 domain were generated using NNK mutagenesis. Variants were transformed into yeast on plasmids and the plasmid barcodes were sequenced at three time points determined by OD. Overlapping paired-end reads were sequenced on Illumina NextSeq and assembled using PEAR.",
        "short_description": "Deep mutational scan of the Src kinase SH4 domain.",
        "title": "Deep mutational scan of Src SH4",
        "keywords": [
            {
                "text": "kinase"
            },
            {
                "text": "growth assay"
            },
            {
                "text": "NNK mutagenesis"
            }
        ],
        "sra_ids": [
            {
                "identifier": "PRJNA464305",
                "url": "http://www.ebi.ac.uk/ena/data/view/PRJNA464305",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30956043",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30956043",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000041-b-1"
        ],
        "experimentset": "urn:mavedb:00000041"
    },
    {
        "creation_date": "2019-02-20",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000033-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of ZFAND3 enhancer in MIN6 cells.",
        "title": "Saturation mutagenesis MPRA of ZFAND3 enhancer",
        "keywords": [
            {
                "text": "enhancer"
            },
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "ZFAND3"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444736",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444736",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000033-a-1"
        ],
        "experimentset": "urn:mavedb:00000033"
    },
    {
        "creation_date": "2021-09-30",
        "modification_date": "2021-09-30",
        "urn": "urn:mavedb:00000076-a",
        "publish_date": "2021-09-30",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This experiment utilized site directed mutagenesis to generate variants in the  carboxyl-terminal tail anchor (TA) on the Fis1p protein within yeast. All possible codons at 27 amino acid positions were assayed for their ability to target the mitochondrial membrane.",
        "method_text": "Degenerate primers and recombination-based cloning were used to create a mutant library of the Fis1p TA protein in a Gal4-sfGFP-Fis1p plasmid. Cells with wild-type-like TA variants would fail to grow, since the Gal4 is localized to the mitochondrial membrane instead of in the nucleus to drive transcription on selective media. Sequencing was performed using a MiSeq Nano (2x150v2).\r\n\r\nThis experiment compares the population grown on supplemented minimal medium (SMM) -Trp -His medium with 20mM 3-aminotriazole to the baseline population grown on synthetic complete (SC) -Trp.",
        "short_description": "Deep mutational scan of the yeast Fis1 tail anchor, SMM -Trp -His medium with 20mM 3-aminotriazole.",
        "title": "Fis1 tail anchor, SMM -Trp -His with 20mM 3-AT",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.5061/dryad.j14r5",
                "url": "http://doi.org/10.5061/dryad.j14r5",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "28007883",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28007883",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-3532-2109"
        ],
        "scoresets": [
            "urn:mavedb:00000076-a-1"
        ],
        "experimentset": "urn:mavedb:00000076"
    },
    {
        "creation_date": "2018-11-09",
        "modification_date": "2019-10-22",
        "urn": "urn:mavedb:00000005-a",
        "publish_date": "2019-10-22",
        "created_by": "0000-0003-1628-9390",
        "modified_by": "0000-0003-1628-9390",
        "extra_metadata": {},
        "abstract_text": "Classical homocystinuria--characterized by excessive levels of total homocysteine in plasma--is caused by primarily-rare variants in the cystathionine-beta-synthase (CBS) gene. With early detection, existing therapies are highly effective, e.g., most patients respond to vitamin B6 therapy. Functional CBS variants, or deleterious variants that respond to vitamin B6, can be detected based on their ability restore growth in yeast cells lacking CYS4 (the yeast ortholog of CBS). Here we describe a comprehensive missense variant effect map for CBS.",
        "method_text": "We reimplemented a previously validated humanized yeast model (Kruger & Cox, PNAS, 1994), confirming that expression of human CBS from the hORFeome collection restores the ability of a yeast cys4&Delta; strain to grow without supplementation of glutathione. Coupling this functional complementation with our recently developed framework for exhaustively mapping functional coding variants (Weile & Sun et al, MSB, 2017), we attempted to test the functional impact as well as the vitamin B6 remediability of all possible missense CBS variants in parallel. \r\n\r\nFirst, we constructed a library of CBS variants using our previously described POPCode mutagenesis method (Weile & Sun et al, MSB, 2017). The variant library, initially generated as a pool of amplicons, was transferred en masse into the appropriate yeast expression vector via two steps of recombinational subcloning.  The resulting library of variant expression clones was then transformed en masse into the yeast cys4 mutant strain. \r\n\r\nNext, pools of transformed yeast cys4 mutant strains were grown competitively in cysteine-lacking medium supplemented with low (0, 1ng/ml) or high (400 ng/ml) concentrations of vitamin B6. Allele frequencies of CBS variants before and after selection were determined by next-generation sequencing. To ensure accuracy of allele frequency estimates, we following the TileSeq approach (Weile & Sun et al, MSB, 2017) in which sequencing is applied to a tiling set of ~100 nt segments of the gene library, enabling sequencing reads from both forward and reverse strands of each template cluster on the flow cell.  Sequencing was performed such that both forward and reverse strands of each nucleotide position were covered by ~2M reads. \r\n\r\nThe sequence analysis code can be found at https://bitbucket.org/rothlabto/tileseq_package\r\n\r\nSee https://www.biorxiv.org/content/early/2018/11/19/473983 for more information.",
        "short_description": "A Deep Mutational Scan of the human Cystathionine beta-Synthase (CBS) using functional complementation in yeast",
        "title": "CBS yeast complementation",
        "keywords": [
            {
                "text": "imputation"
            },
            {
                "text": "Vitamin B6"
            },
            {
                "text": "DMS-TileSeq"
            },
            {
                "text": "homocystinuria"
            },
            {
                "text": "complementation"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [],
        "contributors": [
            "0000-0003-1628-9390"
        ],
        "scoresets": [
            "urn:mavedb:00000005-a-1",
            "urn:mavedb:00000005-a-2",
            "urn:mavedb:00000005-a-5",
            "urn:mavedb:00000005-a-6",
            "urn:mavedb:00000005-a-4",
            "urn:mavedb:00000005-a-3"
        ],
        "experimentset": "urn:mavedb:00000005"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-01-17",
        "urn": "urn:mavedb:00000057-a",
        "publish_date": "2021-01-17",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors used saturation mutagenesis to study the variant effect of Ras, without the regulation of GTPase activating protein (GAP) or guanine nucleotide exchange factor (GEF). The variants were selected using a bacterial two-hybrid strategy.",
        "method_text": "The RAS mutant library was generated by oligonucleotide-directed mutagenesis. The mutant library was transfected into bacteria without GAP or GEF expression and the functioning RAS protein which will bind to GTP as well as Raf. The binding of these molecules can trigger the transcription of an antibiotic resistant factor. The library was separated into three sub-libraries in order to cover the whole RAS gene length which ranges from the residue 2-56, 57-111, and 112-166. These samples were selected individually. The samples in different sub-libraries were barcoded and pooled together for MiSeq sequencing.",
        "short_description": "Selection result of Ras mutants expressed without the GAP or the GEF",
        "title": "Unregulated-Ras",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "28686159",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/28686159",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000057-a-1"
        ],
        "experimentset": "urn:mavedb:00000057"
    },
    {
        "creation_date": "2021-11-04",
        "modification_date": "2021-11-04",
        "urn": "urn:mavedb:00000086-a",
        "publish_date": "2021-11-04",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study examined the fitness effects of single amino acid mutations in TEM-1 β-lactamase in *Escherichia coli* under selection for ampicillin resistance or cefotaxime resistance.",
        "method_text": "The sequence was split into ten non-overlapping subgroups and saturation mutagenesis libraries were created for each using NNS PCR mutagenesis. The PCR products from the mutagenesis were mixed in equimolar ratios and ligated as a single library.\r\n\r\nCells were grown overnight to saturation under non-selective media and then diluted and grown in the presence of the antibiotic to perform the selection.\r\n\r\nSequencing was performed using 75-bp paired-end Illumina reads.",
        "short_description": "Effects of TEM-1 mutations on ampicillin resistance at 10 μg/ml",
        "title": "TEM-1 10 μg/ml Amp",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "25723163",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/25723163",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000086-a-1"
        ],
        "experimentset": "urn:mavedb:00000086"
    },
    {
        "creation_date": "2019-07-29",
        "modification_date": "2019-07-29",
        "urn": "urn:mavedb:00000038-b",
        "publish_date": "2019-07-29",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This study measured the effect of single amino acid changes in ubiquitin on binding to E1 (Uba1). Combined with work from a previous study on the effect of ubiquitin mutations on yeast growth rate, this showed that ubiquitin-E1 binding was not linearly related to growth rate and that mutations in ubiquitin are likely to affect multiple function that modulate growth rate.",
        "method_text": "This experiment used the same library of ubiquitin variants as previously described in Roscoe et al. 2013. The ubiqutin variants were displayed as C-terminal fusions with Aga2-HA and reacted with E1. Bound cells were isolated using FACS and deep sequencing was used to quantify enrichment or depletion of cells in the bound population.\r\n\r\nThe excess E1 assay was performed on two separate sub-regions of ubiquitin.",
        "short_description": "Deep mutational scan of ubiquitin measuring binding to E1 with yeast display with excess E1.",
        "title": "Ubiquitin E1 binding, excess E1",
        "keywords": [
            {
                "text": "Binding"
            },
            {
                "text": "FACS"
            },
            {
                "text": "ubiquitin"
            },
            {
                "text": "E1"
            },
            {
                "text": "yeast display"
            }
        ],
        "sra_ids": [],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "24862281",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/24862281",
                "dbversion": null,
                "dbname": "PubMed"
            },
            {
                "identifier": "23376099",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/23376099",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000038-b-1",
            "urn:mavedb:00000038-b-2"
        ],
        "experimentset": "urn:mavedb:00000038"
    },
    {
        "creation_date": "2020-12-03",
        "modification_date": "2021-04-14",
        "urn": "urn:mavedb:00000061-h",
        "publish_date": "2021-04-14",
        "created_by": "0000-0003-2449-7034",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "The authors generated a library of RAF variant and use the PACS system to test KRAS4b/RAF protein-protein interaction (PPI). The experimental data revealed positions along the binding interface as well as which substitutions are tolerated at each position.",
        "method_text": "A library of RAF variants is generated by introducing mutations into the RAF gene using error prone PCR. The library was introduced into a PACS system. In this system, bacteriophages express mutated RAF proteins and bacteria express KRAS proteins. The KRAS and RAF proteins are engineered and will induce the production of gIII when they are binded which is essential for the replication of phages. The enrichment of RAF mutations are determined at 48h by Illumina sequencing.",
        "short_description": "Measuring the interaction of mutated RAF to RAS by a new phage-assisted continuous selection (PACS) system.",
        "title": "RAF variant selected after 48h",
        "keywords": [],
        "sra_ids": [],
        "doi_ids": [
            {
                "identifier": "10.1021/acschembio.9b00669",
                "url": "https://doi.org/10.1021/acschembio.9b00669",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31808666",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31808666",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0003-2449-7034"
        ],
        "scoresets": [
            "urn:mavedb:00000061-h-1"
        ],
        "experimentset": "urn:mavedb:00000061"
    },
    {
        "creation_date": "2022-07-22",
        "modification_date": "2022-07-22",
        "urn": "urn:mavedb:00000097-m",
        "publish_date": "2022-07-22",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0003-1474-605X",
        "extra_metadata": {},
        "abstract_text": "This dataset contains the pre-normalization scores for BRCA1 saturation genome editing (SGE) data from exon 17, replicate 1. Variants were assayed based on viability in HAP1 cells after direct editing of the endogenous BRCA1 locus using CRISPR-based editing.",
        "method_text": "Oligo pools containing all possible SNVs in the exon were synthesized and cloned into plasmids, creating an SNV library for the exon. These contained the SNV edits being assayed and a fixed synonymous substitution to prevent re-editing by Cas9 after successful repair. HAP1 cells were co-transfected with a plasmid containing Cas9 and a guide RNA. Cells were grown and sampled at 5 days and 11 days. The 5 day time point was used to correct for positional bias in the function scores and for calculating RNA scores. The 11 day time point was used to calculate function scores. Samples were sequenced using Illumina NextSeq or MiSeq platform.",
        "short_description": "BRCA1 SGE exon 17 replicate 1 pre-normalization scores",
        "title": "BRCA1 SGE Exon 17 Replicate 1",
        "keywords": [
            {
                "text": "SGE"
            }
        ],
        "sra_ids": [
            {
                "identifier": "GSE117159",
                "url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117159",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [],
        "pubmed_ids": [
            {
                "identifier": "30209399",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/30209399",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X"
        ],
        "scoresets": [
            "urn:mavedb:00000097-m-1"
        ],
        "experimentset": "urn:mavedb:00000097"
    },
    {
        "creation_date": "2019-02-19",
        "modification_date": "2019-11-21",
        "urn": "urn:mavedb:00000031-a",
        "publish_date": "2019-02-20",
        "created_by": "0000-0003-1474-605X",
        "modified_by": "0000-0002-2032-6679",
        "extra_metadata": {},
        "abstract_text": "This study performed saturation mutagenesis on disease-associated enhancer and promoter regions and measured the effect of each mutation using massively parallel reporter assays (MPRA). The data describe potentially pathogenic mutations as well as the density of putative functional bases in each of the regulatory elements.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "method_text": "Sequences containing mutations were generated using error-prone PCR. Each library contained 50,000-2,000,000 constructs per target, which included nearly all possible single nucleotide changes as well as many single base pair deletions. Variants were tagged with 15 or 20 base pair barcodes 3' of the target region. Promoters were inserted into pGL4.11 vectors and enhancers were inserted into pGL4.23 enhancers such that they would drive expression of the luciferase reporter gene. RNA barcodes were counted using targeted RT-PCR and Illumina sequencing, and DNA barcodes were counted using targeted PCR and Illumina sequencing. Long variant sequences were associate with barcodes using subassembly.\r\n\r\nAs described by <https://www.biorxiv.org/content/10.1101/505362v1>",
        "short_description": "Saturation mutagenesis MPRA of TERT promoter in HEK293T cells.",
        "title": "Saturation mutagenesis MPRA of TERT promoter, HEK",
        "keywords": [
            {
                "text": "barcode sequencing"
            },
            {
                "text": "MPRA"
            },
            {
                "text": "promoter"
            },
            {
                "text": "TERT"
            }
        ],
        "sra_ids": [
            {
                "identifier": "SRX5444734",
                "url": "http://www.ebi.ac.uk/ena/data/view/SRX5444734",
                "dbversion": null,
                "dbname": "SRA"
            }
        ],
        "doi_ids": [
            {
                "identifier": "10.1038/s41467-019-11526-w",
                "url": "https://doi.org/10.1038/s41467-019-11526-w",
                "dbversion": null,
                "dbname": "DOI"
            },
            {
                "identifier": "10.17605/OSF.IO/75B2M",
                "url": "https://doi.org/10.17605/OSF.IO/75B2M",
                "dbversion": null,
                "dbname": "DOI"
            }
        ],
        "pubmed_ids": [
            {
                "identifier": "31395865",
                "url": "http://www.ncbi.nlm.nih.gov/pubmed/31395865",
                "dbversion": null,
                "dbname": "PubMed"
            }
        ],
        "contributors": [
            "0000-0003-1474-605X",
            "0000-0002-2032-6679"
        ],
        "scoresets": [
            "urn:mavedb:00000031-a-1"
        ],
        "experimentset": "urn:mavedb:00000031"
    }
]
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