{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8736JDCM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8736JDCM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_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 [IGVFSM0705YYHP](/in-vitro-systems/IGVFSM0705YYHP/) 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/IGVFSM0705YYHP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0705YYHP](/in-vitro-systems/IGVFSM0705YYHP/) 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/IGVFSM0705YYHP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8736JDCM](/measurement-sets/IGVFDS8736JDCM/) 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/IGVFDS8736JDCM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8736JDCM](/measurement-sets/IGVFDS8736JDCM/) has sequence file(s) [IGVFFI1579EYXF](/sequence-files/IGVFFI1579EYXF/), [IGVFFI6324OAUI](/sequence-files/IGVFFI6324OAUI/), [IGVFFI0302IJDC](/sequence-files/IGVFFI0302IJDC/), [IGVFFI4108LCGL](/sequence-files/IGVFFI4108LCGL/), [IGVFFI6982MJUE](/sequence-files/IGVFFI6982MJUE/), [IGVFFI0774VUGE](/sequence-files/IGVFFI0774VUGE/), [IGVFFI2344MPYS](/sequence-files/IGVFFI2344MPYS/), [IGVFFI3218MAEC](/sequence-files/IGVFFI3218MAEC/), [IGVFFI5037OSTC](/sequence-files/IGVFFI5037OSTC/), [IGVFFI1605RKIL](/sequence-files/IGVFFI1605RKIL/), [IGVFFI2143YPRZ](/sequence-files/IGVFFI2143YPRZ/), [IGVFFI3059ZNIK](/sequence-files/IGVFFI3059ZNIK/), [IGVFFI9515NXDE](/sequence-files/IGVFFI9515NXDE/), [IGVFFI5082PMYW](/sequence-files/IGVFFI5082PMYW/), [IGVFFI2220TWYV](/sequence-files/IGVFFI2220TWYV/), [IGVFFI2252WMRB](/sequence-files/IGVFFI2252WMRB/), [IGVFFI2429ZXKM](/sequence-files/IGVFFI2429ZXKM/), [IGVFFI8907BLPS](/sequence-files/IGVFFI8907BLPS/), [IGVFFI4463GBLF](/sequence-files/IGVFFI4463GBLF/), [IGVFFI1261VPKE](/sequence-files/IGVFFI1261VPKE/), [IGVFFI1620IQSV](/sequence-files/IGVFFI1620IQSV/), [IGVFFI2455UNEY](/sequence-files/IGVFFI2455UNEY/), [IGVFFI6764QMWO](/sequence-files/IGVFFI6764QMWO/), [IGVFFI4206TNWZ](/sequence-files/IGVFFI4206TNWZ/), [IGVFFI8241SECN](/sequence-files/IGVFFI8241SECN/), [IGVFFI8471LHMT](/sequence-files/IGVFFI8471LHMT/), [IGVFFI0446CTYE](/sequence-files/IGVFFI0446CTYE/), [IGVFFI1626KEIY](/sequence-files/IGVFFI1626KEIY/), [IGVFFI6931AEIN](/sequence-files/IGVFFI6931AEIN/), [IGVFFI9685UXUY](/sequence-files/IGVFFI9685UXUY/), [IGVFFI5611GKGA](/sequence-files/IGVFFI5611GKGA/), [IGVFFI8008AVTJ](/sequence-files/IGVFFI8008AVTJ/), [IGVFFI8505XFDQ](/sequence-files/IGVFFI8505XFDQ/), [IGVFFI9099LFJU](/sequence-files/IGVFFI9099LFJU/), [IGVFFI6153JLTF](/sequence-files/IGVFFI6153JLTF/), [IGVFFI6739IQIO](/sequence-files/IGVFFI6739IQIO/), [IGVFFI9226FTHE](/sequence-files/IGVFFI9226FTHE/), [IGVFFI2688SNAC](/sequence-files/IGVFFI2688SNAC/), [IGVFFI6805LACU](/sequence-files/IGVFFI6805LACU/), [IGVFFI8352EATF](/sequence-files/IGVFFI8352EATF/), [IGVFFI5997XBIN](/sequence-files/IGVFFI5997XBIN/), [IGVFFI1380UWLD](/sequence-files/IGVFFI1380UWLD/), [IGVFFI4408DEAJ](/sequence-files/IGVFFI4408DEAJ/), [IGVFFI8627JYIU](/sequence-files/IGVFFI8627JYIU/), [IGVFFI6096PQOZ](/sequence-files/IGVFFI6096PQOZ/), [IGVFFI5588KHSS](/sequence-files/IGVFFI5588KHSS/), [IGVFFI5088SUNH](/sequence-files/IGVFFI5088SUNH/), [IGVFFI6990KYYK](/sequence-files/IGVFFI6990KYYK/) 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/IGVFDS8736JDCM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8736JDCM](/measurement-sets/IGVFDS8736JDCM/) has sequence file(s): [IGVFFI1579EYXF](/sequence-files/IGVFFI1579EYXF/), [IGVFFI6324OAUI](/sequence-files/IGVFFI6324OAUI/), [IGVFFI0302IJDC](/sequence-files/IGVFFI0302IJDC/), [IGVFFI4108LCGL](/sequence-files/IGVFFI4108LCGL/), [IGVFFI6982MJUE](/sequence-files/IGVFFI6982MJUE/), [IGVFFI0774VUGE](/sequence-files/IGVFFI0774VUGE/), [IGVFFI2344MPYS](/sequence-files/IGVFFI2344MPYS/), [IGVFFI3218MAEC](/sequence-files/IGVFFI3218MAEC/), [IGVFFI5037OSTC](/sequence-files/IGVFFI5037OSTC/), [IGVFFI1605RKIL](/sequence-files/IGVFFI1605RKIL/), [IGVFFI2143YPRZ](/sequence-files/IGVFFI2143YPRZ/), [IGVFFI3059ZNIK](/sequence-files/IGVFFI3059ZNIK/), [IGVFFI9515NXDE](/sequence-files/IGVFFI9515NXDE/), [IGVFFI5082PMYW](/sequence-files/IGVFFI5082PMYW/), [IGVFFI2220TWYV](/sequence-files/IGVFFI2220TWYV/), [IGVFFI2252WMRB](/sequence-files/IGVFFI2252WMRB/), [IGVFFI2429ZXKM](/sequence-files/IGVFFI2429ZXKM/), [IGVFFI8907BLPS](/sequence-files/IGVFFI8907BLPS/), [IGVFFI4463GBLF](/sequence-files/IGVFFI4463GBLF/), [IGVFFI1261VPKE](/sequence-files/IGVFFI1261VPKE/), [IGVFFI1620IQSV](/sequence-files/IGVFFI1620IQSV/), [IGVFFI2455UNEY](/sequence-files/IGVFFI2455UNEY/), [IGVFFI6764QMWO](/sequence-files/IGVFFI6764QMWO/), [IGVFFI4206TNWZ](/sequence-files/IGVFFI4206TNWZ/), [IGVFFI8241SECN](/sequence-files/IGVFFI8241SECN/), [IGVFFI8471LHMT](/sequence-files/IGVFFI8471LHMT/), [IGVFFI0446CTYE](/sequence-files/IGVFFI0446CTYE/), [IGVFFI1626KEIY](/sequence-files/IGVFFI1626KEIY/), [IGVFFI6931AEIN](/sequence-files/IGVFFI6931AEIN/), [IGVFFI9685UXUY](/sequence-files/IGVFFI9685UXUY/), [IGVFFI5611GKGA](/sequence-files/IGVFFI5611GKGA/), [IGVFFI8008AVTJ](/sequence-files/IGVFFI8008AVTJ/), [IGVFFI8505XFDQ](/sequence-files/IGVFFI8505XFDQ/), [IGVFFI9099LFJU](/sequence-files/IGVFFI9099LFJU/), [IGVFFI6153JLTF](/sequence-files/IGVFFI6153JLTF/), [IGVFFI6739IQIO](/sequence-files/IGVFFI6739IQIO/), [IGVFFI9226FTHE](/sequence-files/IGVFFI9226FTHE/), [IGVFFI2688SNAC](/sequence-files/IGVFFI2688SNAC/), [IGVFFI6805LACU](/sequence-files/IGVFFI6805LACU/), [IGVFFI8352EATF](/sequence-files/IGVFFI8352EATF/), [IGVFFI5997XBIN](/sequence-files/IGVFFI5997XBIN/), [IGVFFI1380UWLD](/sequence-files/IGVFFI1380UWLD/), [IGVFFI4408DEAJ](/sequence-files/IGVFFI4408DEAJ/), [IGVFFI8627JYIU](/sequence-files/IGVFFI8627JYIU/), [IGVFFI6096PQOZ](/sequence-files/IGVFFI6096PQOZ/), [IGVFFI5588KHSS](/sequence-files/IGVFFI5588KHSS/), [IGVFFI5088SUNH](/sequence-files/IGVFFI5088SUNH/), [IGVFFI6990KYYK](/sequence-files/IGVFFI6990KYYK/) 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/IGVFDS8736JDCM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8736JDCM](/measurement-sets/IGVFDS8736JDCM/) 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/IGVFDS8736JDCM/"
}
]
},
"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": "2023-11-30T22:50:06.248256+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/IGVFFI1579EYXF/",
"accession": "IGVFFI1579EYXF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:47:18.126939+00:00",
"file_format": "fastq",
"file_size": 1627843,
"href": "/sequence-files/IGVFFI1579EYXF/@@download/IGVFFI1579EYXF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dde2fc23-56a5-48a5-b977-c5ef2a585c4c/IGVFFI1579EYXF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep4_S316_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6324OAUI/",
"accession": "IGVFFI6324OAUI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:50:02.944260+00:00",
"file_format": "fastq",
"file_size": 6113504,
"href": "/sequence-files/IGVFFI6324OAUI/@@download/IGVFFI6324OAUI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d6c95fa9-b75d-4df8-b410-fdaa0fec302b/IGVFFI6324OAUI.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-BinC-PCRrep8_S320_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0302IJDC/",
"accession": "IGVFFI0302IJDC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:44:06.879786+00:00",
"file_format": "fastq",
"file_size": 5269821,
"href": "/sequence-files/IGVFFI0302IJDC/@@download/IGVFFI0302IJDC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bdb814e8-e39d-419b-9b09-5ce5c7c25c3b/IGVFFI0302IJDC.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-BinC-PCRrep1_S313_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4108LCGL/",
"accession": "IGVFFI4108LCGL",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:46:43.543183+00:00",
"file_format": "fastq",
"file_size": 1534447,
"href": "/sequence-files/IGVFFI4108LCGL/@@download/IGVFFI4108LCGL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/14ee705a-b9a7-4977-aee2-9c558887673f/IGVFFI4108LCGL.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6982MJUE/",
"accession": "IGVFFI6982MJUE",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:44:41.722987+00:00",
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"file_size": 5199622,
"href": "/sequence-files/IGVFFI6982MJUE/@@download/IGVFFI6982MJUE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6bb3938e-ac1a-44c9-94d7-b2c6672c0175/IGVFFI6982MJUE.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-BinC-PCRrep10_S322_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0774VUGE/",
"accession": "IGVFFI0774VUGE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:44:15.585438+00:00",
"file_format": "fastq",
"file_size": 6481065,
"href": "/sequence-files/IGVFFI0774VUGE/@@download/IGVFFI0774VUGE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5e552d6a-f31b-473d-a845-3b1d0ac39a43/IGVFFI0774VUGE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep1_S313_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2344MPYS/",
"accession": "IGVFFI2344MPYS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep12_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:45:33.794859+00:00",
"file_format": "fastq",
"file_size": 1329905,
"href": "/sequence-files/IGVFFI2344MPYS/@@download/IGVFFI2344MPYS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5a842bc4-3e92-4861-aa35-6b688206531f/IGVFFI2344MPYS.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep12_S324_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3218MAEC/",
"accession": "IGVFFI3218MAEC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:47:00.862931+00:00",
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"file_size": 5232192,
"href": "/sequence-files/IGVFFI3218MAEC/@@download/IGVFFI3218MAEC.fastq.gz",
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},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep3_S315_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5037OSTC/",
"accession": "IGVFFI5037OSTC",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep3-BinC-PCRrep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:49:45.544900+00:00",
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"file_size": 1392653,
"href": "/sequence-files/IGVFFI5037OSTC/@@download/IGVFFI5037OSTC.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-BinC-PCRrep8_S320_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1605RKIL/",
"accession": "IGVFFI1605RKIL",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:48:27.674631+00:00",
"file_format": "fastq",
"file_size": 1526010,
"href": "/sequence-files/IGVFFI1605RKIL/@@download/IGVFFI1605RKIL.fastq.gz",
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"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-BinC-PCRrep6_S318_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2143YPRZ/",
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"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "178cbb30-67ac-423b-811d-e9c77b097bd1"
}