{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS0821YMMV/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0821YMMV",
"aliases": [
"charles-gersbach:cd8-tcell-perturb-seq-crispr-grna-construct-lib-set"
],
"applied_to_samples": [
{
"@id": "/primary-cells/IGVFSM3795JDHP/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3795JDHP",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep1"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7605NZFO/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)"
},
{
"@id": "/primary-cells/IGVFSM2105CLXS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2105CLXS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep3"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO4425KRAT/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"summary": "CRISPRa Sa-dCas9-VP64"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)"
},
{
"@id": "/primary-cells/IGVFSM5189UBOI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5189UBOI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep3"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO4425KRAT/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)"
},
{
"@id": "/primary-cells/IGVFSM6223YCQV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6223YCQV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep2"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6082RNLT/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"summary": "CRISPRa Sa-dCas9-VP64"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)"
},
{
"@id": "/primary-cells/IGVFSM8036VPRU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8036VPRU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep1"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7605NZFO/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"summary": "CRISPRa Sa-dCas9-VP64"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)"
},
{
"@id": "/primary-cells/IGVFSM2747RJFY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747RJFY",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep2"
],
"classifications": [
"primary cell"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6082RNLT/",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"summary": "CRISPRi Sa-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)"
}
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS0821YMMV](/construct-library-sets/IGVFDS0821YMMV/) has revoked subobject tabular file [IGVFFI1405WMSH](/tabular-files/IGVFFI1405WMSH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS0821YMMV/"
},
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS0821YMMV](/construct-library-sets/IGVFDS0821YMMV/) has in progress subobject tabular file [IGVFFI2489BLJI](/tabular-files/IGVFFI2489BLJI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS0821YMMV/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS0821YMMV](/construct-library-sets/IGVFDS0821YMMV/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS0821YMMV/"
}
]
},
"average_guide_coverage": 1.33,
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2023-11-08T19:22:26.815519+00:00",
"documents": [
"/documents/ee0564e2-3d03-4c94-bcb3-39d2bbd2d588/",
"/documents/27ec67ed-40bb-4090-93db-a7b2d9fc1861/"
],
"file_set_type": "guide library",
"files": [],
"guide_type": "sgRNA",
"input_for": [],
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1405WMSH/",
"accession": "IGVFFI1405WMSH",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-metadata"
],
"content_type": "guide RNA sequences",
"file_format": "tsv",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2489BLJI/",
"accession": "IGVFFI2489BLJI",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-metadata-v3"
],
"content_type": "guide RNA sequences",
"file_format": "tsv",
"upload_status": "invalidated"
}
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"release_timestamp": "2024-10-18T19:49:56.930821+00:00",
"schema_version": "10",
"scope": "genes",
"selection_criteria": [
"transcription start sites"
],
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000156127/",
"geneid": "ENSG00000156127",
"name": "basic leucine zipper ATF-like transcription factor",
"symbol": "BATF",
"synonyms": [
"basic leucine zipper transcriptional factor ATF-like",
"activating transcription factor B",
"B-cell-activating transcription factor",
"basic leucine zipper transcription factor, ATF-like",
"SFA2",
"SF-HT-activated gene 2 protein",
"B-ATF",
"SFA-2",
"BATF1"
]
},
{
"@id": "/genes/ENSG00000123685/",
"geneid": "ENSG00000123685",
"name": "basic leucine zipper ATF-like transcription factor 3",
"symbol": "BATF3",
"synonyms": [
"B-ATF-3",
"JUNDM1",
"Jun dimerization protein p21SNFT",
"basic leucine zipper transcriptional factor ATF-like 3",
"SNFT",
"21-kD small nuclear factor isolated from T cells",
"Jun dimerization protein 1",
"21 kDa small nuclear factor isolated from T-cells",
"JDP1",
"basic leucine zipper transcription factor, ATF-like 3"
]
},
{
"@id": "/genes/ENSG00000134107/",
"geneid": "ENSG00000134107",
"name": "basic helix-loop-helix family member e40",
"symbol": "BHLHE40",
"synonyms": [
"class B basic helix-loop-helix protein 2",
"SHARP2",
"differentially expressed in chondrocytes protein 1",
"differentially expressed in chondrocytes 1",
"basic helix-loop-helix domain containing, class B, 2",
"SHARP-2",
"HLHB2",
"BHLHB2",
"differentiated embryo chondrocyte expressed gene 1",
"DEC1",
"stimulated by retinoic acid gene 13 protein",
"class E basic helix-loop-helix protein 40",
"STRA13",
"enhancer-of-split and hairy-related protein 2",
"Stra14",
"Clast5"
]
},
{
"@id": "/genes/ENSG00000095794/",
"geneid": "ENSG00000095794",
"name": "cAMP responsive element modulator",
"symbol": "CREM",
"synonyms": [
"cAMP response element modulator",
"inducible cAMP early repressor ICER",
"CREM 2beta-a protein",
"CREM-2",
"ICER",
"cAMP-responsive element modulator",
"hCREM-2",
"CREM 2alpha-b protein"
]
},
{
"@id": "/genes/ENSG00000163508/",
"geneid": "ENSG00000163508",
"name": "eomesodermin",
"symbol": "EOMES",
"synonyms": [
"TBR2",
"T-box brain protein 2",
"eomesodermin homolog"
]
},
{
"@id": "/genes/ENSG00000151702/",
"geneid": "ENSG00000151702",
"name": "Fli-1 proto-oncogene, ETS transcription factor",
"symbol": "FLI1",
"synonyms": [
"EWSR2",
"Friend leukemia integration 1 transcription factor",
"transcription factor ERGB",
"FLI-1",
"BDPLT21",
"Friend leukemia virus integration 1",
"SIC-1",
"Ewing sarcoma breakpoint region 2"
]
},
{
"@id": "/genes/ENSG00000186564/",
"geneid": "ENSG00000186564",
"name": "forkhead box D2",
"symbol": "FOXD2",
"synonyms": [
"forkhead, drosophila, homolog-like 17",
"FREAC9",
"FREAC-9",
"forkhead-related transcription factor 9",
"FKHL17",
"forkhead-like 17",
"forkhead-related protein FKHL17",
"forkhead box protein D2",
"forkhead-related activator 9"
]
},
{
"@id": "/genes/ENSG00000150907/",
"geneid": "ENSG00000150907",
"name": "forkhead box O1",
"symbol": "FOXO1",
"synonyms": [
"forkhead box protein O1",
"FOXO1A",
"forkhead box protein O1A",
"FKHR",
"forkhead, Drosophila, homolog of, in rhabdomyosarcoma",
"FKH1"
]
},
{
"@id": "/genes/ENSG00000154727/",
"geneid": "ENSG00000154727",
"name": "GA binding protein transcription factor subunit alpha",
"symbol": "GABPA",
"synonyms": [
"NRF2",
"E4TF1-60",
"GA binding protein transcription factor alpha subunit 60kDa",
"NRF2A",
"GABP subunit alpha",
"GA-binding protein alpha chain",
"E4TF1A",
"NFT2",
"nuclear respiratory factor 2 subunit alpha",
"transcription factor E4TF1-60",
"human nuclear respiratory factor-2 subunit alpha",
"RCH04A07",
"nuclear respiratory factor 2 alpha subunit"
]
},
{
"@id": "/genes/ENSG00000177374/",
"geneid": "ENSG00000177374",
"name": "HIC ZBTB transcriptional repressor 1",
"symbol": "HIC1",
"synonyms": [
"hypermethylated in cancer 1 protein",
"hic-1",
"ZBTB29",
"zinc finger and BTB domain-containing protein 29",
"ZNF901",
"hypermethylated in cancer 1"
]
},
{
"@id": "/genes/ENSG00000168310/",
"geneid": "ENSG00000168310",
"name": "interferon regulatory factor 2",
"symbol": "IRF2",
"synonyms": [
"interferon regulatory factor 2",
"IRF-2"
]
},
{
"@id": "/genes/ENSG00000177606/",
"geneid": "ENSG00000177606",
"name": "Jun proto-oncogene, AP-1 transcription factor subunit",
"symbol": "JUN",
"synonyms": [
"jun oncogene",
"cJUN",
"enhancer-binding protein AP1",
"p39",
"proto-oncogene cJun",
"activator protein 1",
"transcription factor AP-1 subunit Jun",
"transcription factor AP-1",
"v-jun avian sarcoma virus 17 oncogene homolog",
"Jun activation domain binding protein",
"proto-oncogene c-Jun",
"v-jun sarcoma virus 17 oncogene homolog",
"transcription factor Jun",
"AP1",
"c-Jun",
"AP-1"
]
},
{
"@id": "/genes/ENSG00000118513/",
"geneid": "ENSG00000118513",
"name": "MYB proto-oncogene, transcription factor",
"symbol": "MYB",
"synonyms": [
"Cmyb",
"MYB-GATA1 fusion protein",
"oncogene AMV",
"proto-oncogene c-Myb",
"v-myb avian myeloblastosis viral oncogene homolog",
"transcriptional activator Myb",
"c-myb_CDS",
"efg",
"c-myb"
]
},
{
"@id": "/genes/ENSG00000072736/",
"geneid": "ENSG00000072736",
"name": "nuclear factor of activated T cells 3",
"symbol": "NFATC3",
"synonyms": [
"NFATX",
"NF-ATc3",
"n339260",
"NF-AT4c",
"T cell transcription factor NFAT4",
"NFAT4",
"nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3",
"nuclear factor of activated T-cells, cytoplasmic 3"
]
},
{
"@id": "/genes/ENSG00000082641/",
"geneid": "ENSG00000082641",
"name": "NFE2 like bZIP transcription factor 1",
"symbol": "NFE2L1",
"synonyms": [
"LCR-F1",
"transcription factor HBZ17",
"nuclear factor, erythroid 2 like 1",
"NFE2-related factor 1",
"NF-E2-related factor 1",
"nuclear factor, erythroid derived 2, like 1",
"TCF-11",
"protein NRF1, p120 form",
"endoplasmic reticulum membrane sensor NFE2L1",
"locus control region-factor 1",
"transcription factor 11 (basic leucine zipper type)",
"NRF1",
"NRF-1",
"nuclear factor erythroid 2-related factor 1",
"TCF11",
"transcription factor LCR-F1"
]
},
{
"@id": "/genes/ENSG00000126368/",
"geneid": "ENSG00000126368",
"name": "nuclear receptor subfamily 1 group D member 1",
"symbol": "NR1D1",
"synonyms": [
"rev-erbA-alpha",
"REVERBalpha",
"REVERBA",
"nuclear receptor Rev-ErbA-alpha",
"ear-1",
"nuclear receptor subfamily 1 group D member 1",
"Rev-ErbAalpha",
"THRA1",
"hRev",
"V-erbA-related protein 1",
"THRAL",
"EAR1"
]
},
{
"@id": "/genes/ENSG00000123358/",
"geneid": "ENSG00000123358",
"name": "nuclear receptor subfamily 4 group A member 1",
"symbol": "NR4A1",
"synonyms": [
"hormone receptor",
"NP10",
"growth factor-inducible nuclear protein N10",
"N10",
"NUR77",
"NAK-1",
"testicular receptor 3",
"NGFIB",
"GFRP1",
"HMR",
"orphan nuclear receptor HMR",
"TR3 orphan receptor",
"TR3",
"steroid receptor TR3",
"nuclear receptor subfamily 4 group A member 1",
"early response protein NAK1",
"ST-59",
"nuclear hormone receptor NUR/77",
"orphan nuclear receptor TR3"
]
},
{
"@id": "/genes/ENSG00000143190/",
"geneid": "ENSG00000143190",
"name": "POU class 2 homeobox 1",
"symbol": "POU2F1",
"synonyms": [
"OTF1",
"oct-1B",
"NF-A1",
"octamer-binding protein 1",
"Oct1Z",
"OTF-1",
"oct-1",
"octamer-binding transcription factor 1",
"OCT1",
"POU domain, class 2, transcription factor 1",
"Octamer-binding transcription factor-1"
]
},
{
"@id": "/genes/ENSG00000124782/",
"geneid": "ENSG00000124782",
"name": "ras responsive element binding protein 1",
"symbol": "RREB1",
"synonyms": [
"DNA-binding protein",
"HNT",
"Zep-1",
"LZ321",
"RREB-1",
"zinc finger motif enhancer-binding protein 1",
"raf-responsive zinc finger protein LZ321",
"hindsight homolog",
"FINB",
"ras-responsive element-binding protein 1",
"finger protein in nuclear bodies"
]
},
{
"@id": "/genes/ENSG00000152284/",
"geneid": "ENSG00000152284",
"name": "transcription factor 7 like 1",
"symbol": "TCF7L1",
"synonyms": [
"transcription factor 7-like 1",
"TCF3",
"HMG box transcription factor 3",
"transcription factor 7-like 1 (T-cell specific, HMG-box)",
"TCF-3"
]
},
{
"@id": "/genes/ENSG00000184517/",
"geneid": "ENSG00000184517",
"name": "ZFP1 zinc finger protein",
"symbol": "ZFP1",
"synonyms": [
"zinc finger protein 1 homolog",
"ZNF475",
"zinc finger protein 475"
]
},
{
"@id": "/genes/ENSG00000112182/",
"geneid": "ENSG00000112182",
"name": "BTB domain and CNC homolog 2",
"symbol": "BACH2",
"synonyms": [
"IMD60",
"BTBD25",
"BTB and CNC homology 1, basic leucine zipper transcription factor 2",
"BTB and CNC homolog 2",
"transcription regulator protein BACH2"
]
},
{
"@id": "/genes/ENSG00000127528/",
"geneid": "ENSG00000127528",
"name": "KLF transcription factor 2",
"symbol": "KLF2",
"synonyms": [
"Kruppel-like factor LKLF",
"LKLF",
"Kruppel like factor 2",
"Krueppel-like factor 2",
"lung Kruppel-like factor",
"lung Kruppel-like zinc finger transcription factor",
"lung krueppel-like factor",
"Kruppel-like factor 2 (lung)"
]
},
{
"@id": "/genes/ENSG00000130816/",
"geneid": "ENSG00000130816",
"name": "DNA methyltransferase 1",
"symbol": "DNMT1",
"synonyms": [
"MCMT",
"CXXC9",
"AIM",
"DNA methyltransferase HsaI",
"HSN1E",
"ADCADN",
"DNA (cytosine-5)-methyltransferase 1",
"m.HsaI",
"CXXC-type zinc finger protein 9",
"DNA (cytosine-5-)-methyltransferase 1",
"DNMT",
"DNA MTase HsaI"
]
}
],
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"summary": "Guide (sgRNA) library targeting transcription start sites in 24 genes",
"tiling_modality": "sparse peaks",
"uuid": "d30dd13f-75f9-4fdd-87a5-5f0ff6e35a06"
}