{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6267YRNH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6267YRNH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD_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": "mismatched status",
"detail": "Released in vitro system [IGVFSM3394FCPH](/in-vitro-systems/IGVFSM3394FCPH/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3394FCPH/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3394FCPH](/in-vitro-systems/IGVFSM3394FCPH/) 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/IGVFSM3394FCPH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6267YRNH](/measurement-sets/IGVFDS6267YRNH/) 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/IGVFDS6267YRNH/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6267YRNH](/measurement-sets/IGVFDS6267YRNH/) has sequence file(s) [IGVFFI4067UUSI](/sequence-files/IGVFFI4067UUSI/), [IGVFFI4901CITF](/sequence-files/IGVFFI4901CITF/), [IGVFFI9773KZXY](/sequence-files/IGVFFI9773KZXY/), [IGVFFI5195WRZW](/sequence-files/IGVFFI5195WRZW/), [IGVFFI6475PTNS](/sequence-files/IGVFFI6475PTNS/), [IGVFFI6210YESJ](/sequence-files/IGVFFI6210YESJ/), [IGVFFI8136VPPB](/sequence-files/IGVFFI8136VPPB/), [IGVFFI3906VRIJ](/sequence-files/IGVFFI3906VRIJ/), [IGVFFI0676URKU](/sequence-files/IGVFFI0676URKU/), [IGVFFI3953CRLL](/sequence-files/IGVFFI3953CRLL/), [IGVFFI4817ARZB](/sequence-files/IGVFFI4817ARZB/), [IGVFFI1375EDJF](/sequence-files/IGVFFI1375EDJF/), [IGVFFI2588AXXW](/sequence-files/IGVFFI2588AXXW/), [IGVFFI3684LCNA](/sequence-files/IGVFFI3684LCNA/), [IGVFFI0737WUQP](/sequence-files/IGVFFI0737WUQP/), [IGVFFI8230PQJJ](/sequence-files/IGVFFI8230PQJJ/), [IGVFFI4488UJSM](/sequence-files/IGVFFI4488UJSM/), [IGVFFI8230ERRR](/sequence-files/IGVFFI8230ERRR/), [IGVFFI8435EMLD](/sequence-files/IGVFFI8435EMLD/), [IGVFFI4114CMRD](/sequence-files/IGVFFI4114CMRD/), [IGVFFI1013XTPI](/sequence-files/IGVFFI1013XTPI/), [IGVFFI1713MUGN](/sequence-files/IGVFFI1713MUGN/), [IGVFFI9121IGRO](/sequence-files/IGVFFI9121IGRO/), [IGVFFI3752UGNK](/sequence-files/IGVFFI3752UGNK/), [IGVFFI9722PDEX](/sequence-files/IGVFFI9722PDEX/), [IGVFFI4827WISX](/sequence-files/IGVFFI4827WISX/), [IGVFFI0646LPXR](/sequence-files/IGVFFI0646LPXR/), [IGVFFI2397OGWW](/sequence-files/IGVFFI2397OGWW/), [IGVFFI8900YUVW](/sequence-files/IGVFFI8900YUVW/), [IGVFFI0996LKFZ](/sequence-files/IGVFFI0996LKFZ/), [IGVFFI6922KTRA](/sequence-files/IGVFFI6922KTRA/), [IGVFFI0273KKME](/sequence-files/IGVFFI0273KKME/), [IGVFFI4684KBXY](/sequence-files/IGVFFI4684KBXY/), [IGVFFI0338PYWL](/sequence-files/IGVFFI0338PYWL/), [IGVFFI3841AJXD](/sequence-files/IGVFFI3841AJXD/), [IGVFFI7387ETFG](/sequence-files/IGVFFI7387ETFG/), [IGVFFI3065KWEP](/sequence-files/IGVFFI3065KWEP/), [IGVFFI2777XJUK](/sequence-files/IGVFFI2777XJUK/), [IGVFFI2824CBDP](/sequence-files/IGVFFI2824CBDP/), [IGVFFI1532LAJW](/sequence-files/IGVFFI1532LAJW/), [IGVFFI0947PEWE](/sequence-files/IGVFFI0947PEWE/), [IGVFFI7174FPNE](/sequence-files/IGVFFI7174FPNE/), [IGVFFI0348MCPO](/sequence-files/IGVFFI0348MCPO/), [IGVFFI3540AZOR](/sequence-files/IGVFFI3540AZOR/), [IGVFFI2966KRCC](/sequence-files/IGVFFI2966KRCC/), [IGVFFI5431QIHK](/sequence-files/IGVFFI5431QIHK/), [IGVFFI3124MVTX](/sequence-files/IGVFFI3124MVTX/), [IGVFFI7651WQJW](/sequence-files/IGVFFI7651WQJW/) 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/IGVFDS6267YRNH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6267YRNH](/measurement-sets/IGVFDS6267YRNH/) has sequence file(s): [IGVFFI4067UUSI](/sequence-files/IGVFFI4067UUSI/), [IGVFFI4901CITF](/sequence-files/IGVFFI4901CITF/), [IGVFFI9773KZXY](/sequence-files/IGVFFI9773KZXY/), [IGVFFI5195WRZW](/sequence-files/IGVFFI5195WRZW/), [IGVFFI6475PTNS](/sequence-files/IGVFFI6475PTNS/), [IGVFFI6210YESJ](/sequence-files/IGVFFI6210YESJ/), [IGVFFI8136VPPB](/sequence-files/IGVFFI8136VPPB/), [IGVFFI3906VRIJ](/sequence-files/IGVFFI3906VRIJ/), [IGVFFI0676URKU](/sequence-files/IGVFFI0676URKU/), [IGVFFI3953CRLL](/sequence-files/IGVFFI3953CRLL/), [IGVFFI4817ARZB](/sequence-files/IGVFFI4817ARZB/), [IGVFFI1375EDJF](/sequence-files/IGVFFI1375EDJF/), [IGVFFI2588AXXW](/sequence-files/IGVFFI2588AXXW/), [IGVFFI3684LCNA](/sequence-files/IGVFFI3684LCNA/), [IGVFFI0737WUQP](/sequence-files/IGVFFI0737WUQP/), [IGVFFI8230PQJJ](/sequence-files/IGVFFI8230PQJJ/), [IGVFFI4488UJSM](/sequence-files/IGVFFI4488UJSM/), [IGVFFI8230ERRR](/sequence-files/IGVFFI8230ERRR/), [IGVFFI8435EMLD](/sequence-files/IGVFFI8435EMLD/), [IGVFFI4114CMRD](/sequence-files/IGVFFI4114CMRD/), [IGVFFI1013XTPI](/sequence-files/IGVFFI1013XTPI/), [IGVFFI1713MUGN](/sequence-files/IGVFFI1713MUGN/), [IGVFFI9121IGRO](/sequence-files/IGVFFI9121IGRO/), [IGVFFI3752UGNK](/sequence-files/IGVFFI3752UGNK/), [IGVFFI9722PDEX](/sequence-files/IGVFFI9722PDEX/), [IGVFFI4827WISX](/sequence-files/IGVFFI4827WISX/), [IGVFFI0646LPXR](/sequence-files/IGVFFI0646LPXR/), [IGVFFI2397OGWW](/sequence-files/IGVFFI2397OGWW/), [IGVFFI8900YUVW](/sequence-files/IGVFFI8900YUVW/), [IGVFFI0996LKFZ](/sequence-files/IGVFFI0996LKFZ/), [IGVFFI6922KTRA](/sequence-files/IGVFFI6922KTRA/), [IGVFFI0273KKME](/sequence-files/IGVFFI0273KKME/), [IGVFFI4684KBXY](/sequence-files/IGVFFI4684KBXY/), [IGVFFI0338PYWL](/sequence-files/IGVFFI0338PYWL/), [IGVFFI3841AJXD](/sequence-files/IGVFFI3841AJXD/), [IGVFFI7387ETFG](/sequence-files/IGVFFI7387ETFG/), [IGVFFI3065KWEP](/sequence-files/IGVFFI3065KWEP/), [IGVFFI2777XJUK](/sequence-files/IGVFFI2777XJUK/), [IGVFFI2824CBDP](/sequence-files/IGVFFI2824CBDP/), [IGVFFI1532LAJW](/sequence-files/IGVFFI1532LAJW/), [IGVFFI0947PEWE](/sequence-files/IGVFFI0947PEWE/), [IGVFFI7174FPNE](/sequence-files/IGVFFI7174FPNE/), [IGVFFI0348MCPO](/sequence-files/IGVFFI0348MCPO/), [IGVFFI3540AZOR](/sequence-files/IGVFFI3540AZOR/), [IGVFFI2966KRCC](/sequence-files/IGVFFI2966KRCC/), [IGVFFI5431QIHK](/sequence-files/IGVFFI5431QIHK/), [IGVFFI3124MVTX](/sequence-files/IGVFFI3124MVTX/), [IGVFFI7651WQJW](/sequence-files/IGVFFI7651WQJW/) 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/IGVFDS6267YRNH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6267YRNH](/measurement-sets/IGVFDS6267YRNH/) 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/IGVFDS6267YRNH/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:07.148810+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/IGVFFI4067UUSI/",
"accession": "IGVFFI4067UUSI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:56:34.368251+00:00",
"file_format": "fastq",
"file_size": 1407557,
"href": "/sequence-files/IGVFFI4067UUSI/@@download/IGVFFI4067UUSI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ede00d3c-c100-4415-befb-0e506ea3fe99/IGVFFI4067UUSI.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep8_S332_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4901CITF/",
"accession": "IGVFFI4901CITF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:51:03.472669+00:00",
"file_format": "fastq",
"file_size": 5189771,
"href": "/sequence-files/IGVFFI4901CITF/@@download/IGVFFI4901CITF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6a462fe1-5753-420d-8190-64f43c8ab15a/IGVFFI4901CITF.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep1_S325_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9773KZXY/",
"accession": "IGVFFI9773KZXY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:54:49.291481+00:00",
"file_format": "fastq",
"file_size": 1555015,
"href": "/sequence-files/IGVFFI9773KZXY/@@download/IGVFFI9773KZXY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/05408bed-c8f4-4480-9cab-e8d3d9f1e800/IGVFFI9773KZXY.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep5_S329_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5195WRZW/",
"accession": "IGVFFI5195WRZW",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:56:51.786804+00:00",
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"file_size": 4769515,
"href": "/sequence-files/IGVFFI5195WRZW/@@download/IGVFFI5195WRZW.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6475PTNS/",
"accession": "IGVFFI6475PTNS",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:56:07.865198+00:00",
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"href": "/sequence-files/IGVFFI6475PTNS/@@download/IGVFFI6475PTNS.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6210YESJ/",
"accession": "IGVFFI6210YESJ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:57:09.300816+00:00",
"file_format": "fastq",
"file_size": 1462350,
"href": "/sequence-files/IGVFFI6210YESJ/@@download/IGVFFI6210YESJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/97bba62c-8980-4f76-8c9d-acf4f29a7ba6/IGVFFI6210YESJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep9_S333_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8136VPPB/",
"accession": "IGVFFI8136VPPB",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:50:46.233083+00:00",
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"file_size": 1563093,
"href": "/sequence-files/IGVFFI8136VPPB/@@download/IGVFFI8136VPPB.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3906VRIJ/",
"accession": "IGVFFI3906VRIJ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:54:40.539968+00:00",
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"href": "/sequence-files/IGVFFI3906VRIJ/@@download/IGVFFI3906VRIJ.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0676URKU/",
"accession": "IGVFFI0676URKU",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:54:58.041179+00:00",
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"href": "/sequence-files/IGVFFI0676URKU/@@download/IGVFFI0676URKU.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3953CRLL/",
"accession": "IGVFFI3953CRLL",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:51:38.237457+00:00",
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"href": "/sequence-files/IGVFFI3953CRLL/@@download/IGVFFI3953CRLL.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinD-PCRrep10_S334_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4817ARZB/",
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"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "bced11bd-f79f-4dbe-be46-346aaddffe0f"
}