{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0894QRYX](/in-vitro-systems/IGVFSM0894QRYX/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM0894QRYX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS4989HPTW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) has sequence file(s) [IGVFFI2581VJGU](/sequence-files/IGVFFI2581VJGU/), [IGVFFI4400NUZL](/sequence-files/IGVFFI4400NUZL/), [IGVFFI1787VTHF](/sequence-files/IGVFFI1787VTHF/), [IGVFFI8924WIBE](/sequence-files/IGVFFI8924WIBE/), [IGVFFI0445HZBU](/sequence-files/IGVFFI0445HZBU/), [IGVFFI6121VYZF](/sequence-files/IGVFFI6121VYZF/), [IGVFFI2456ZPNX](/sequence-files/IGVFFI2456ZPNX/), [IGVFFI7071KMDT](/sequence-files/IGVFFI7071KMDT/), [IGVFFI3409EVBJ](/sequence-files/IGVFFI3409EVBJ/), [IGVFFI5763USVR](/sequence-files/IGVFFI5763USVR/), [IGVFFI5926QOUF](/sequence-files/IGVFFI5926QOUF/), [IGVFFI1936ZBLG](/sequence-files/IGVFFI1936ZBLG/), [IGVFFI3638DTXQ](/sequence-files/IGVFFI3638DTXQ/), [IGVFFI8676JDHE](/sequence-files/IGVFFI8676JDHE/), [IGVFFI6091JGXB](/sequence-files/IGVFFI6091JGXB/), [IGVFFI5807UNLW](/sequence-files/IGVFFI5807UNLW/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS4989HPTW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) has sequence file(s): [IGVFFI2581VJGU](/sequence-files/IGVFFI2581VJGU/), [IGVFFI4400NUZL](/sequence-files/IGVFFI4400NUZL/), [IGVFFI1787VTHF](/sequence-files/IGVFFI1787VTHF/), [IGVFFI8924WIBE](/sequence-files/IGVFFI8924WIBE/), [IGVFFI0445HZBU](/sequence-files/IGVFFI0445HZBU/), [IGVFFI6121VYZF](/sequence-files/IGVFFI6121VYZF/), [IGVFFI2456ZPNX](/sequence-files/IGVFFI2456ZPNX/), [IGVFFI7071KMDT](/sequence-files/IGVFFI7071KMDT/), [IGVFFI3409EVBJ](/sequence-files/IGVFFI3409EVBJ/), [IGVFFI5763USVR](/sequence-files/IGVFFI5763USVR/), [IGVFFI5926QOUF](/sequence-files/IGVFFI5926QOUF/), [IGVFFI1936ZBLG](/sequence-files/IGVFFI1936ZBLG/), [IGVFFI3638DTXQ](/sequence-files/IGVFFI3638DTXQ/), [IGVFFI8676JDHE](/sequence-files/IGVFFI8676JDHE/), [IGVFFI6091JGXB](/sequence-files/IGVFFI6091JGXB/), [IGVFFI5807UNLW](/sequence-files/IGVFFI5807UNLW/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS4989HPTW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS4989HPTW/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS4989HPTW](/measurement-sets/IGVFDS4989HPTW/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS4989HPTW/"
}
]
},
"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_for": [
{
"@id": "/measurement-sets/IGVFDS8504HJPW/",
"accession": "IGVFDS8504HJPW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0471SKEE/",
"accession": "IGVFDS0471SKEE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2059ELNJ/",
"accession": "IGVFDS2059ELNJ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7083JDYN/",
"accession": "IGVFDS7083JDYN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6071XLAA/",
"accession": "IGVFDS6071XLAA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9915OTKB/",
"accession": "IGVFDS9915OTKB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6176JWXB/",
"accession": "IGVFDS6176JWXB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5341DFHM/",
"accession": "IGVFDS5341DFHM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7933SDSN/",
"accession": "IGVFDS7933SDSN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8050CYYG/",
"accession": "IGVFDS8050CYYG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2690TJJM/",
"accession": "IGVFDS2690TJJM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3823MIDB/",
"accession": "IGVFDS3823MIDB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0621TDYK/",
"accession": "IGVFDS0621TDYK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8825HZQT/",
"accession": "IGVFDS8825HZQT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8518OHPN/",
"accession": "IGVFDS8518OHPN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9126DKWW/",
"accession": "IGVFDS9126DKWW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1183IGHQ/",
"accession": "IGVFDS1183IGHQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5892ADAN/",
"accession": "IGVFDS5892ADAN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2890JPBI/",
"accession": "IGVFDS2890JPBI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0816EELG/",
"accession": "IGVFDS0816EELG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4670KYYZ/",
"accession": "IGVFDS4670KYYZ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8339LZYX/",
"accession": "IGVFDS8339LZYX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1285SAVV/",
"accession": "IGVFDS1285SAVV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8629CPYB/",
"accession": "IGVFDS8629CPYB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5601DSMT/",
"accession": "IGVFDS5601DSMT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6229XAIE/",
"accession": "IGVFDS6229XAIE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3368XILR/",
"accession": "IGVFDS3368XILR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5477WNYP/",
"accession": "IGVFDS5477WNYP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2074JWFW/",
"accession": "IGVFDS2074JWFW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9345IHWB/",
"accession": "IGVFDS9345IHWB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9179GDAL/",
"accession": "IGVFDS9179GDAL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2972VXMB/",
"accession": "IGVFDS2972VXMB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1144XHLC/",
"accession": "IGVFDS1144XHLC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4386IYQY/",
"accession": "IGVFDS4386IYQY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2708HTXW/",
"accession": "IGVFDS2708HTXW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9571BWRT/",
"accession": "IGVFDS9571BWRT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4823GFCR/",
"accession": "IGVFDS4823GFCR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4736IKQS/",
"accession": "IGVFDS4736IKQS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7952EIJE/",
"accession": "IGVFDS7952EIJE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5405RYGU/",
"accession": "IGVFDS5405RYGU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD_AmpliconSequencing"
],
"status": "released"
}
],
"control_type": "untransfected",
"creation_timestamp": "2023-11-30T22:48:51.997826+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2581VJGU/",
"accession": "IGVFFI2581VJGU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:42:26.531425+00:00",
"file_format": "fastq",
"file_size": 965353,
"href": "/sequence-files/IGVFFI2581VJGU/@@download/IGVFFI2581VJGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dd3c8c72-fee5-45f0-b84b-639c6c46dba4/IGVFFI2581VJGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinNeg-PCRrep4_S404_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4400NUZL/",
"accession": "IGVFFI4400NUZL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:40:54.319846+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI4400NUZL/@@download/IGVFFI4400NUZL.fastq.gz",
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"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinNeg-PCRrep1_S393_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1787VTHF/",
"accession": "IGVFFI1787VTHF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:41:31.116624+00:00",
"file_format": "fastq",
"file_size": 3105883,
"href": "/sequence-files/IGVFFI1787VTHF/@@download/IGVFFI1787VTHF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/eebd629f-7bb0-4cdb-99e3-a5eb34d18fdf/IGVFFI1787VTHF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinNeg-PCRrep2_S394_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8924WIBE/",
"accession": "IGVFFI8924WIBE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:40:45.056177+00:00",
"file_format": "fastq",
"file_size": 969042,
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