{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5477WNYP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5477WNYP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003133/",
"term_name": "cas mediated mutagenesis"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9885ZFLQ](/in-vitro-systems/IGVFSM9885ZFLQ/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9885ZFLQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) has sequence file(s): [IGVFFI2605DQIM](/sequence-files/IGVFFI2605DQIM/), [IGVFFI3187QDMT](/sequence-files/IGVFFI3187QDMT/), [IGVFFI1912LVJT](/sequence-files/IGVFFI1912LVJT/), [IGVFFI6169EWXA](/sequence-files/IGVFFI6169EWXA/), [IGVFFI5949EOUJ](/sequence-files/IGVFFI5949EOUJ/), [IGVFFI0991WDRN](/sequence-files/IGVFFI0991WDRN/), [IGVFFI6927GQDY](/sequence-files/IGVFFI6927GQDY/), [IGVFFI9861XHPY](/sequence-files/IGVFFI9861XHPY/), [IGVFFI7883JRKY](/sequence-files/IGVFFI7883JRKY/), [IGVFFI1281VXNX](/sequence-files/IGVFFI1281VXNX/), [IGVFFI0648GPZW](/sequence-files/IGVFFI0648GPZW/), [IGVFFI5309KPDI](/sequence-files/IGVFFI5309KPDI/), [IGVFFI9512FNAC](/sequence-files/IGVFFI9512FNAC/), [IGVFFI5628XVFI](/sequence-files/IGVFFI5628XVFI/), [IGVFFI7223VMRP](/sequence-files/IGVFFI7223VMRP/), [IGVFFI5171BCDJ](/sequence-files/IGVFFI5171BCDJ/), [IGVFFI2054TDYJ](/sequence-files/IGVFFI2054TDYJ/), [IGVFFI9099SLBG](/sequence-files/IGVFFI9099SLBG/), [IGVFFI3264LXAW](/sequence-files/IGVFFI3264LXAW/), [IGVFFI5800FGLP](/sequence-files/IGVFFI5800FGLP/), [IGVFFI5785QLPT](/sequence-files/IGVFFI5785QLPT/), [IGVFFI5610EVMF](/sequence-files/IGVFFI5610EVMF/), [IGVFFI5144QHLR](/sequence-files/IGVFFI5144QHLR/), [IGVFFI7910CVXJ](/sequence-files/IGVFFI7910CVXJ/), [IGVFFI2797ANPA](/sequence-files/IGVFFI2797ANPA/), [IGVFFI3585OFZJ](/sequence-files/IGVFFI3585OFZJ/), [IGVFFI3940WJXI](/sequence-files/IGVFFI3940WJXI/), [IGVFFI8539GMBL](/sequence-files/IGVFFI8539GMBL/), [IGVFFI1956RNGN](/sequence-files/IGVFFI1956RNGN/), [IGVFFI4560NNFM](/sequence-files/IGVFFI4560NNFM/), [IGVFFI5848YMAZ](/sequence-files/IGVFFI5848YMAZ/), [IGVFFI9665RFUR](/sequence-files/IGVFFI9665RFUR/), [IGVFFI0374IWLU](/sequence-files/IGVFFI0374IWLU/), [IGVFFI4151NBWZ](/sequence-files/IGVFFI4151NBWZ/), [IGVFFI6487NWKX](/sequence-files/IGVFFI6487NWKX/), [IGVFFI0042NSBU](/sequence-files/IGVFFI0042NSBU/), [IGVFFI5390HCVI](/sequence-files/IGVFFI5390HCVI/), [IGVFFI6736ZEKX](/sequence-files/IGVFFI6736ZEKX/), [IGVFFI8177EEPG](/sequence-files/IGVFFI8177EEPG/), [IGVFFI1178XOXU](/sequence-files/IGVFFI1178XOXU/), [IGVFFI2110KAHF](/sequence-files/IGVFFI2110KAHF/), [IGVFFI4255CFZV](/sequence-files/IGVFFI4255CFZV/), [IGVFFI8551UDTB](/sequence-files/IGVFFI8551UDTB/), [IGVFFI3566YLHM](/sequence-files/IGVFFI3566YLHM/), [IGVFFI9516NNFX](/sequence-files/IGVFFI9516NNFX/), [IGVFFI2393OTSX](/sequence-files/IGVFFI2393OTSX/), [IGVFFI8003TTWY](/sequence-files/IGVFFI8003TTWY/), [IGVFFI1792RKRX](/sequence-files/IGVFFI1792RKRX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5477WNYP/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_CRISPR_assay_missing_cell_sorting_auxiliary_set",
"path": "/measurement-sets/IGVFDS5477WNYP/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) has no variant sequencing `auxiliary_sets`. Variant FlowFISH measurement sets are expected to link to a variant sequencing auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_Variant_FlowFISH_missing_variant_sequencing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5477WNYP/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) has no `targeted_genes`. ChIP-seq and FISH-based assays are expected to specify targeted gene(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS5477WNYP/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5477WNYP](/measurement-sets/IGVFDS5477WNYP/) has sequence file(s) [IGVFFI2605DQIM](/sequence-files/IGVFFI2605DQIM/), [IGVFFI3187QDMT](/sequence-files/IGVFFI3187QDMT/), [IGVFFI1912LVJT](/sequence-files/IGVFFI1912LVJT/), [IGVFFI6169EWXA](/sequence-files/IGVFFI6169EWXA/), [IGVFFI5949EOUJ](/sequence-files/IGVFFI5949EOUJ/), [IGVFFI0991WDRN](/sequence-files/IGVFFI0991WDRN/), [IGVFFI6927GQDY](/sequence-files/IGVFFI6927GQDY/), [IGVFFI9861XHPY](/sequence-files/IGVFFI9861XHPY/), [IGVFFI7883JRKY](/sequence-files/IGVFFI7883JRKY/), [IGVFFI1281VXNX](/sequence-files/IGVFFI1281VXNX/), [IGVFFI0648GPZW](/sequence-files/IGVFFI0648GPZW/), [IGVFFI5309KPDI](/sequence-files/IGVFFI5309KPDI/), [IGVFFI9512FNAC](/sequence-files/IGVFFI9512FNAC/), [IGVFFI5628XVFI](/sequence-files/IGVFFI5628XVFI/), [IGVFFI7223VMRP](/sequence-files/IGVFFI7223VMRP/), [IGVFFI5171BCDJ](/sequence-files/IGVFFI5171BCDJ/), [IGVFFI2054TDYJ](/sequence-files/IGVFFI2054TDYJ/), [IGVFFI9099SLBG](/sequence-files/IGVFFI9099SLBG/), [IGVFFI3264LXAW](/sequence-files/IGVFFI3264LXAW/), [IGVFFI5800FGLP](/sequence-files/IGVFFI5800FGLP/), [IGVFFI5785QLPT](/sequence-files/IGVFFI5785QLPT/), [IGVFFI5610EVMF](/sequence-files/IGVFFI5610EVMF/), [IGVFFI5144QHLR](/sequence-files/IGVFFI5144QHLR/), [IGVFFI7910CVXJ](/sequence-files/IGVFFI7910CVXJ/), [IGVFFI2797ANPA](/sequence-files/IGVFFI2797ANPA/), [IGVFFI3585OFZJ](/sequence-files/IGVFFI3585OFZJ/), [IGVFFI3940WJXI](/sequence-files/IGVFFI3940WJXI/), [IGVFFI8539GMBL](/sequence-files/IGVFFI8539GMBL/), [IGVFFI1956RNGN](/sequence-files/IGVFFI1956RNGN/), [IGVFFI4560NNFM](/sequence-files/IGVFFI4560NNFM/), [IGVFFI5848YMAZ](/sequence-files/IGVFFI5848YMAZ/), [IGVFFI9665RFUR](/sequence-files/IGVFFI9665RFUR/), [IGVFFI0374IWLU](/sequence-files/IGVFFI0374IWLU/), [IGVFFI4151NBWZ](/sequence-files/IGVFFI4151NBWZ/), [IGVFFI6487NWKX](/sequence-files/IGVFFI6487NWKX/), [IGVFFI0042NSBU](/sequence-files/IGVFFI0042NSBU/), [IGVFFI5390HCVI](/sequence-files/IGVFFI5390HCVI/), [IGVFFI6736ZEKX](/sequence-files/IGVFFI6736ZEKX/), [IGVFFI8177EEPG](/sequence-files/IGVFFI8177EEPG/), [IGVFFI1178XOXU](/sequence-files/IGVFFI1178XOXU/), [IGVFFI2110KAHF](/sequence-files/IGVFFI2110KAHF/), [IGVFFI4255CFZV](/sequence-files/IGVFFI4255CFZV/), [IGVFFI8551UDTB](/sequence-files/IGVFFI8551UDTB/), [IGVFFI3566YLHM](/sequence-files/IGVFFI3566YLHM/), [IGVFFI9516NNFX](/sequence-files/IGVFFI9516NNFX/), [IGVFFI2393OTSX](/sequence-files/IGVFFI2393OTSX/), [IGVFFI8003TTWY](/sequence-files/IGVFFI8003TTWY/), [IGVFFI1792RKRX](/sequence-files/IGVFFI1792RKRX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5477WNYP/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:01.572913+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
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{
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"accession": "IGVFFI2605DQIM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD-PCRrep10_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:38:36.220635+00:00",
"file_format": "fastq",
"file_size": 1606600,
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD-PCRrep10_S142_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3187QDMT/",
"accession": "IGVFFI3187QDMT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD-PCRrep12_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:39:54.096018+00:00",
"file_format": "fastq",
"file_size": 1538050,
"href": "/sequence-files/IGVFFI3187QDMT/@@download/IGVFFI3187QDMT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/43b1201e-179c-4d25-aaac-6ec711a21849/IGVFFI3187QDMT.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1912LVJT/",
"accession": "IGVFFI1912LVJT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD-PCRrep12_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:40:21.801498+00:00",
"file_format": "fastq",
"file_size": 6849807,
"href": "/sequence-files/IGVFFI1912LVJT/@@download/IGVFFI1912LVJT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b9317a02-4cf1-4095-b8d4-8e12ca5a1194/IGVFFI1912LVJT.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6169EWXA/",
"accession": "IGVFFI6169EWXA",
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],
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"creation_timestamp": "2023-12-05T20:41:45.528304+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5949EOUJ/",
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"aliases": [
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],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:42:31.198125+00:00",
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"href": "/sequence-files/IGVFFI5949EOUJ/@@download/IGVFFI5949EOUJ.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0991WDRN/",
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],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:38:45.301013+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6927GQDY/",
"accession": "IGVFFI6927GQDY",
"aliases": [
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],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:38:17.888701+00:00",
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"href": "/sequence-files/IGVFFI6927GQDY/@@download/IGVFFI6927GQDY.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9861XHPY/",
"accession": "IGVFFI9861XHPY",
"aliases": [
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],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:39:25.777692+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7883JRKY/",
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"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1281VXNX/",
"accession": "IGVFFI1281VXNX",
"aliases": [
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],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:40:49.541810+00:00",
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"file_size": 3642479,
"href": "/sequence-files/IGVFFI1281VXNX/@@download/IGVFFI1281VXNX.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0648GPZW/",
"accession": "IGVFFI0648GPZW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD-PCRrep4_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:41:54.498411+00:00",
"file_format": "fastq",
"file_size": 938090,
"href": "/sequence-files/IGVFFI0648GPZW/@@download/IGVFFI0648GPZW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0c7cf47e-bd4f-4741-94d4-63266896870f/IGVFFI0648GPZW.fastq.gz",
"sequencing_platform": {
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