{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7933SDSN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7933SDSN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB_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 [IGVFSM3035HZXX](/in-vitro-systems/IGVFSM3035HZXX/) 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/IGVFSM3035HZXX/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3035HZXX](/in-vitro-systems/IGVFSM3035HZXX/) 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/IGVFSM3035HZXX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7933SDSN](/measurement-sets/IGVFDS7933SDSN/) 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/IGVFDS7933SDSN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7933SDSN](/measurement-sets/IGVFDS7933SDSN/) has sequence file(s) [IGVFFI7856MTUN](/sequence-files/IGVFFI7856MTUN/), [IGVFFI2068IWLE](/sequence-files/IGVFFI2068IWLE/), [IGVFFI5542JBYK](/sequence-files/IGVFFI5542JBYK/), [IGVFFI2764CXQB](/sequence-files/IGVFFI2764CXQB/), [IGVFFI7348VBDI](/sequence-files/IGVFFI7348VBDI/), [IGVFFI3789JGZM](/sequence-files/IGVFFI3789JGZM/), [IGVFFI5991FMCF](/sequence-files/IGVFFI5991FMCF/), [IGVFFI0088MAAD](/sequence-files/IGVFFI0088MAAD/), [IGVFFI3977QBRI](/sequence-files/IGVFFI3977QBRI/), [IGVFFI8228JKPA](/sequence-files/IGVFFI8228JKPA/), [IGVFFI7822RMOA](/sequence-files/IGVFFI7822RMOA/), [IGVFFI3496OLIA](/sequence-files/IGVFFI3496OLIA/), [IGVFFI4731PKPW](/sequence-files/IGVFFI4731PKPW/), [IGVFFI4866GHCG](/sequence-files/IGVFFI4866GHCG/), [IGVFFI7889KYOP](/sequence-files/IGVFFI7889KYOP/), [IGVFFI1457JCQH](/sequence-files/IGVFFI1457JCQH/), [IGVFFI3737JJGF](/sequence-files/IGVFFI3737JJGF/), [IGVFFI7471NLRD](/sequence-files/IGVFFI7471NLRD/), [IGVFFI1301NZEM](/sequence-files/IGVFFI1301NZEM/), [IGVFFI7159NXVI](/sequence-files/IGVFFI7159NXVI/), [IGVFFI6241UDKW](/sequence-files/IGVFFI6241UDKW/), [IGVFFI9280LARL](/sequence-files/IGVFFI9280LARL/), [IGVFFI2614HUWS](/sequence-files/IGVFFI2614HUWS/), [IGVFFI9894IYQV](/sequence-files/IGVFFI9894IYQV/), [IGVFFI7267OFJX](/sequence-files/IGVFFI7267OFJX/), [IGVFFI9064TVQM](/sequence-files/IGVFFI9064TVQM/), [IGVFFI0993BCAJ](/sequence-files/IGVFFI0993BCAJ/), [IGVFFI8524JTCM](/sequence-files/IGVFFI8524JTCM/), [IGVFFI2967UUCI](/sequence-files/IGVFFI2967UUCI/), [IGVFFI4426BINF](/sequence-files/IGVFFI4426BINF/), [IGVFFI1494DYOX](/sequence-files/IGVFFI1494DYOX/), [IGVFFI9695WNIE](/sequence-files/IGVFFI9695WNIE/), [IGVFFI8266OKSW](/sequence-files/IGVFFI8266OKSW/), [IGVFFI6534GIAR](/sequence-files/IGVFFI6534GIAR/), [IGVFFI9492OGSA](/sequence-files/IGVFFI9492OGSA/), [IGVFFI0349SQOT](/sequence-files/IGVFFI0349SQOT/), [IGVFFI8848BMJG](/sequence-files/IGVFFI8848BMJG/), [IGVFFI1779XXYO](/sequence-files/IGVFFI1779XXYO/), [IGVFFI3845WRSC](/sequence-files/IGVFFI3845WRSC/), [IGVFFI9157RMLD](/sequence-files/IGVFFI9157RMLD/), [IGVFFI0182DYGL](/sequence-files/IGVFFI0182DYGL/), [IGVFFI6589AVJA](/sequence-files/IGVFFI6589AVJA/), [IGVFFI0424MXOX](/sequence-files/IGVFFI0424MXOX/), [IGVFFI3508QZQO](/sequence-files/IGVFFI3508QZQO/), [IGVFFI3195JFDX](/sequence-files/IGVFFI3195JFDX/), [IGVFFI6790WFYI](/sequence-files/IGVFFI6790WFYI/), [IGVFFI4225AIUG](/sequence-files/IGVFFI4225AIUG/), [IGVFFI3382PKLE](/sequence-files/IGVFFI3382PKLE/) 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/IGVFDS7933SDSN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7933SDSN](/measurement-sets/IGVFDS7933SDSN/) has sequence file(s): [IGVFFI7856MTUN](/sequence-files/IGVFFI7856MTUN/), [IGVFFI2068IWLE](/sequence-files/IGVFFI2068IWLE/), [IGVFFI5542JBYK](/sequence-files/IGVFFI5542JBYK/), [IGVFFI2764CXQB](/sequence-files/IGVFFI2764CXQB/), [IGVFFI7348VBDI](/sequence-files/IGVFFI7348VBDI/), [IGVFFI3789JGZM](/sequence-files/IGVFFI3789JGZM/), [IGVFFI5991FMCF](/sequence-files/IGVFFI5991FMCF/), [IGVFFI0088MAAD](/sequence-files/IGVFFI0088MAAD/), [IGVFFI3977QBRI](/sequence-files/IGVFFI3977QBRI/), [IGVFFI8228JKPA](/sequence-files/IGVFFI8228JKPA/), [IGVFFI7822RMOA](/sequence-files/IGVFFI7822RMOA/), [IGVFFI3496OLIA](/sequence-files/IGVFFI3496OLIA/), [IGVFFI4731PKPW](/sequence-files/IGVFFI4731PKPW/), [IGVFFI4866GHCG](/sequence-files/IGVFFI4866GHCG/), [IGVFFI7889KYOP](/sequence-files/IGVFFI7889KYOP/), [IGVFFI1457JCQH](/sequence-files/IGVFFI1457JCQH/), [IGVFFI3737JJGF](/sequence-files/IGVFFI3737JJGF/), [IGVFFI7471NLRD](/sequence-files/IGVFFI7471NLRD/), [IGVFFI1301NZEM](/sequence-files/IGVFFI1301NZEM/), [IGVFFI7159NXVI](/sequence-files/IGVFFI7159NXVI/), [IGVFFI6241UDKW](/sequence-files/IGVFFI6241UDKW/), [IGVFFI9280LARL](/sequence-files/IGVFFI9280LARL/), [IGVFFI2614HUWS](/sequence-files/IGVFFI2614HUWS/), [IGVFFI9894IYQV](/sequence-files/IGVFFI9894IYQV/), [IGVFFI7267OFJX](/sequence-files/IGVFFI7267OFJX/), [IGVFFI9064TVQM](/sequence-files/IGVFFI9064TVQM/), [IGVFFI0993BCAJ](/sequence-files/IGVFFI0993BCAJ/), [IGVFFI8524JTCM](/sequence-files/IGVFFI8524JTCM/), [IGVFFI2967UUCI](/sequence-files/IGVFFI2967UUCI/), [IGVFFI4426BINF](/sequence-files/IGVFFI4426BINF/), [IGVFFI1494DYOX](/sequence-files/IGVFFI1494DYOX/), [IGVFFI9695WNIE](/sequence-files/IGVFFI9695WNIE/), [IGVFFI8266OKSW](/sequence-files/IGVFFI8266OKSW/), [IGVFFI6534GIAR](/sequence-files/IGVFFI6534GIAR/), [IGVFFI9492OGSA](/sequence-files/IGVFFI9492OGSA/), [IGVFFI0349SQOT](/sequence-files/IGVFFI0349SQOT/), [IGVFFI8848BMJG](/sequence-files/IGVFFI8848BMJG/), [IGVFFI1779XXYO](/sequence-files/IGVFFI1779XXYO/), [IGVFFI3845WRSC](/sequence-files/IGVFFI3845WRSC/), [IGVFFI9157RMLD](/sequence-files/IGVFFI9157RMLD/), [IGVFFI0182DYGL](/sequence-files/IGVFFI0182DYGL/), [IGVFFI6589AVJA](/sequence-files/IGVFFI6589AVJA/), [IGVFFI0424MXOX](/sequence-files/IGVFFI0424MXOX/), [IGVFFI3508QZQO](/sequence-files/IGVFFI3508QZQO/), [IGVFFI3195JFDX](/sequence-files/IGVFFI3195JFDX/), [IGVFFI6790WFYI](/sequence-files/IGVFFI6790WFYI/), [IGVFFI4225AIUG](/sequence-files/IGVFFI4225AIUG/), [IGVFFI3382PKLE](/sequence-files/IGVFFI3382PKLE/) 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/IGVFDS7933SDSN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7933SDSN](/measurement-sets/IGVFDS7933SDSN/) 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/IGVFDS7933SDSN/"
}
]
},
"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/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:04.619473+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": [
{
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"accession": "IGVFFI7856MTUN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB-PCRrep11_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:55:30.509224+00:00",
"file_format": "fastq",
"file_size": 1360558,
"href": "/sequence-files/IGVFFI7856MTUN/@@download/IGVFFI7856MTUN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4f40bcc9-e7ea-4a4d-b997-c17070d786d0/IGVFFI7856MTUN.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-FFrep4-BinB-PCRrep11_S167_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2068IWLE/",
"accession": "IGVFFI2068IWLE",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:54:35.120581+00:00",
"file_format": "fastq",
"file_size": 4020378,
"href": "/sequence-files/IGVFFI2068IWLE/@@download/IGVFFI2068IWLE.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB-PCRrep1_S67_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5542JBYK/",
"accession": "IGVFFI5542JBYK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB-PCRrep12_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:55:58.335585+00:00",
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"href": "/sequence-files/IGVFFI5542JBYK/@@download/IGVFFI5542JBYK.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2764CXQB/",
"accession": "IGVFFI2764CXQB",
"aliases": [
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],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T20:58:26.359317+00:00",
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"href": "/sequence-files/IGVFFI2764CXQB/@@download/IGVFFI2764CXQB.fastq.gz",
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI7348VBDI",
"aliases": [
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],
"content_type": "reads",
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},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB-PCRrep10_S166_R2_001.fastq.gz",
"upload_status": "validated"
},
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"@id": "/sequence-files/IGVFFI3789JGZM/",
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"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:56:45.094157+00:00",
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"href": "/sequence-files/IGVFFI3789JGZM/@@download/IGVFFI3789JGZM.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB-PCRrep2_S68_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5991FMCF/",
"accession": "IGVFFI5991FMCF",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:54:16.715704+00:00",
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"href": "/sequence-files/IGVFFI5991FMCF/@@download/IGVFFI5991FMCF.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI0088MAAD",
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3977QBRI/",
"accession": "IGVFFI3977QBRI",
"aliases": [
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],
"content_type": "reads",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8228JKPA/",
"accession": "IGVFFI8228JKPA",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:58:17.147544+00:00",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinB-PCRrep4_S70_R2_001.fastq.gz",
"upload_status": "validated"
},
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"status": "released",
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"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:54:07.586704+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"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": "9f757a98-04d1-4835-9b18-192c1cd727cd"
}