{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4823GFCR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4823GFCR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_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": "Measurement set [IGVFDS4823GFCR](/measurement-sets/IGVFDS4823GFCR/) 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/IGVFDS4823GFCR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4823GFCR](/measurement-sets/IGVFDS4823GFCR/) has sequence file(s) [IGVFFI9325QTXR](/sequence-files/IGVFFI9325QTXR/), [IGVFFI7494MIKK](/sequence-files/IGVFFI7494MIKK/), [IGVFFI4660BALK](/sequence-files/IGVFFI4660BALK/), [IGVFFI0748IVBC](/sequence-files/IGVFFI0748IVBC/), [IGVFFI3482MXNL](/sequence-files/IGVFFI3482MXNL/), [IGVFFI7290QTRZ](/sequence-files/IGVFFI7290QTRZ/), [IGVFFI4905TRRM](/sequence-files/IGVFFI4905TRRM/), [IGVFFI8287CDRW](/sequence-files/IGVFFI8287CDRW/), [IGVFFI4035XOZM](/sequence-files/IGVFFI4035XOZM/), [IGVFFI4590EFMQ](/sequence-files/IGVFFI4590EFMQ/), [IGVFFI9854VTIE](/sequence-files/IGVFFI9854VTIE/), [IGVFFI9431CBDE](/sequence-files/IGVFFI9431CBDE/), [IGVFFI6187OFBV](/sequence-files/IGVFFI6187OFBV/), [IGVFFI6829EFMN](/sequence-files/IGVFFI6829EFMN/), [IGVFFI6733KTID](/sequence-files/IGVFFI6733KTID/), [IGVFFI3960ZWGZ](/sequence-files/IGVFFI3960ZWGZ/), [IGVFFI1894YMEP](/sequence-files/IGVFFI1894YMEP/), [IGVFFI2123RKCD](/sequence-files/IGVFFI2123RKCD/), [IGVFFI7617SZUX](/sequence-files/IGVFFI7617SZUX/), [IGVFFI9066CJDM](/sequence-files/IGVFFI9066CJDM/), [IGVFFI5286KNSP](/sequence-files/IGVFFI5286KNSP/), [IGVFFI6277XNJT](/sequence-files/IGVFFI6277XNJT/), [IGVFFI9356PWMQ](/sequence-files/IGVFFI9356PWMQ/), [IGVFFI6203RINE](/sequence-files/IGVFFI6203RINE/), [IGVFFI0509HQBW](/sequence-files/IGVFFI0509HQBW/), [IGVFFI5534YUBB](/sequence-files/IGVFFI5534YUBB/), [IGVFFI4434GJET](/sequence-files/IGVFFI4434GJET/), [IGVFFI1507YPOH](/sequence-files/IGVFFI1507YPOH/), [IGVFFI0997AGXW](/sequence-files/IGVFFI0997AGXW/), [IGVFFI7462PTDK](/sequence-files/IGVFFI7462PTDK/), [IGVFFI2188JIXY](/sequence-files/IGVFFI2188JIXY/), [IGVFFI6580KAQX](/sequence-files/IGVFFI6580KAQX/), [IGVFFI6920MOMD](/sequence-files/IGVFFI6920MOMD/), [IGVFFI8913FTLL](/sequence-files/IGVFFI8913FTLL/), [IGVFFI2029XCPF](/sequence-files/IGVFFI2029XCPF/), [IGVFFI2188PISQ](/sequence-files/IGVFFI2188PISQ/), [IGVFFI1814RIWT](/sequence-files/IGVFFI1814RIWT/), [IGVFFI4624YRTJ](/sequence-files/IGVFFI4624YRTJ/), [IGVFFI3250MYEW](/sequence-files/IGVFFI3250MYEW/), [IGVFFI9246VBTO](/sequence-files/IGVFFI9246VBTO/), [IGVFFI6968ADID](/sequence-files/IGVFFI6968ADID/), [IGVFFI3097SQMH](/sequence-files/IGVFFI3097SQMH/), [IGVFFI2978XLFR](/sequence-files/IGVFFI2978XLFR/), [IGVFFI9133DXTR](/sequence-files/IGVFFI9133DXTR/), [IGVFFI1714XREB](/sequence-files/IGVFFI1714XREB/), [IGVFFI9062HXWI](/sequence-files/IGVFFI9062HXWI/), [IGVFFI8452QJHH](/sequence-files/IGVFFI8452QJHH/), [IGVFFI9576LPOQ](/sequence-files/IGVFFI9576LPOQ/) 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/IGVFDS4823GFCR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4823GFCR](/measurement-sets/IGVFDS4823GFCR/) has sequence file(s): [IGVFFI9325QTXR](/sequence-files/IGVFFI9325QTXR/), [IGVFFI7494MIKK](/sequence-files/IGVFFI7494MIKK/), [IGVFFI4660BALK](/sequence-files/IGVFFI4660BALK/), [IGVFFI0748IVBC](/sequence-files/IGVFFI0748IVBC/), [IGVFFI3482MXNL](/sequence-files/IGVFFI3482MXNL/), [IGVFFI7290QTRZ](/sequence-files/IGVFFI7290QTRZ/), [IGVFFI4905TRRM](/sequence-files/IGVFFI4905TRRM/), [IGVFFI8287CDRW](/sequence-files/IGVFFI8287CDRW/), [IGVFFI4035XOZM](/sequence-files/IGVFFI4035XOZM/), [IGVFFI4590EFMQ](/sequence-files/IGVFFI4590EFMQ/), [IGVFFI9854VTIE](/sequence-files/IGVFFI9854VTIE/), [IGVFFI9431CBDE](/sequence-files/IGVFFI9431CBDE/), [IGVFFI6187OFBV](/sequence-files/IGVFFI6187OFBV/), [IGVFFI6829EFMN](/sequence-files/IGVFFI6829EFMN/), [IGVFFI6733KTID](/sequence-files/IGVFFI6733KTID/), [IGVFFI3960ZWGZ](/sequence-files/IGVFFI3960ZWGZ/), [IGVFFI1894YMEP](/sequence-files/IGVFFI1894YMEP/), [IGVFFI2123RKCD](/sequence-files/IGVFFI2123RKCD/), [IGVFFI7617SZUX](/sequence-files/IGVFFI7617SZUX/), [IGVFFI9066CJDM](/sequence-files/IGVFFI9066CJDM/), [IGVFFI5286KNSP](/sequence-files/IGVFFI5286KNSP/), [IGVFFI6277XNJT](/sequence-files/IGVFFI6277XNJT/), [IGVFFI9356PWMQ](/sequence-files/IGVFFI9356PWMQ/), [IGVFFI6203RINE](/sequence-files/IGVFFI6203RINE/), [IGVFFI0509HQBW](/sequence-files/IGVFFI0509HQBW/), [IGVFFI5534YUBB](/sequence-files/IGVFFI5534YUBB/), [IGVFFI4434GJET](/sequence-files/IGVFFI4434GJET/), [IGVFFI1507YPOH](/sequence-files/IGVFFI1507YPOH/), [IGVFFI0997AGXW](/sequence-files/IGVFFI0997AGXW/), [IGVFFI7462PTDK](/sequence-files/IGVFFI7462PTDK/), [IGVFFI2188JIXY](/sequence-files/IGVFFI2188JIXY/), [IGVFFI6580KAQX](/sequence-files/IGVFFI6580KAQX/), [IGVFFI6920MOMD](/sequence-files/IGVFFI6920MOMD/), [IGVFFI8913FTLL](/sequence-files/IGVFFI8913FTLL/), [IGVFFI2029XCPF](/sequence-files/IGVFFI2029XCPF/), [IGVFFI2188PISQ](/sequence-files/IGVFFI2188PISQ/), [IGVFFI1814RIWT](/sequence-files/IGVFFI1814RIWT/), [IGVFFI4624YRTJ](/sequence-files/IGVFFI4624YRTJ/), [IGVFFI3250MYEW](/sequence-files/IGVFFI3250MYEW/), [IGVFFI9246VBTO](/sequence-files/IGVFFI9246VBTO/), [IGVFFI6968ADID](/sequence-files/IGVFFI6968ADID/), [IGVFFI3097SQMH](/sequence-files/IGVFFI3097SQMH/), [IGVFFI2978XLFR](/sequence-files/IGVFFI2978XLFR/), [IGVFFI9133DXTR](/sequence-files/IGVFFI9133DXTR/), [IGVFFI1714XREB](/sequence-files/IGVFFI1714XREB/), [IGVFFI9062HXWI](/sequence-files/IGVFFI9062HXWI/), [IGVFFI8452QJHH](/sequence-files/IGVFFI8452QJHH/), [IGVFFI9576LPOQ](/sequence-files/IGVFFI9576LPOQ/) 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/IGVFDS4823GFCR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7460SNVF](/in-vitro-systems/IGVFSM7460SNVF/) 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/IGVFSM7460SNVF/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7460SNVF](/in-vitro-systems/IGVFSM7460SNVF/) 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/IGVFSM7460SNVF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4823GFCR](/measurement-sets/IGVFDS4823GFCR/) 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/IGVFDS4823GFCR/"
}
]
},
"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": "2023-11-30T22:49:24.315429+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/IGVFFI9325QTXR/",
"accession": "IGVFFI9325QTXR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:27:15.435820+00:00",
"file_format": "fastq",
"file_size": 3086781,
"href": "/sequence-files/IGVFFI9325QTXR/@@download/IGVFFI9325QTXR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/30874312-de43-44df-a175-00a9f45978d3/IGVFFI9325QTXR.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-BioRep2-FFrep4-BinA-PCRrep4_S250_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7494MIKK/",
"accession": "IGVFFI7494MIKK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep12_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:25:24.927168+00:00",
"file_format": "fastq",
"file_size": 3304319,
"href": "/sequence-files/IGVFFI7494MIKK/@@download/IGVFFI7494MIKK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/62071aa8-bde7-4a37-80ca-ac316df7fb67/IGVFFI7494MIKK.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-BioRep2-FFrep4-BinA-PCRrep12_S348_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4660BALK/",
"accession": "IGVFFI4660BALK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:23:43.798717+00:00",
"file_format": "fastq",
"file_size": 3583230,
"href": "/sequence-files/IGVFFI4660BALK/@@download/IGVFFI4660BALK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/33efefdf-8996-4375-b797-3814c53626d3/IGVFFI4660BALK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep1_S247_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0748IVBC/",
"accession": "IGVFFI0748IVBC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep11_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:24:30.155010+00:00",
"file_format": "fastq",
"file_size": 807552,
"href": "/sequence-files/IGVFFI0748IVBC/@@download/IGVFFI0748IVBC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f9707c33-0806-458c-ad1b-cb387f198353/IGVFFI0748IVBC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep11_S347_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3482MXNL/",
"accession": "IGVFFI3482MXNL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep10_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:24:20.806976+00:00",
"file_format": "fastq",
"file_size": 3598722,
"href": "/sequence-files/IGVFFI3482MXNL/@@download/IGVFFI3482MXNL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f6f991bb-c2af-43de-b441-6ae0bd09d5a0/IGVFFI3482MXNL.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-BioRep2-FFrep4-BinA-PCRrep10_S346_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7290QTRZ/",
"accession": "IGVFFI7290QTRZ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep9_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:30:10.975102+00:00",
"file_format": "fastq",
"file_size": 825414,
"href": "/sequence-files/IGVFFI7290QTRZ/@@download/IGVFFI7290QTRZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dbd280da-f069-42bb-b201-b38c9751ccc3/IGVFFI7290QTRZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep9_S345_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4905TRRM/",
"accession": "IGVFFI4905TRRM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep12_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:25:06.949490+00:00",
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"file_size": 876023,
"href": "/sequence-files/IGVFFI4905TRRM/@@download/IGVFFI4905TRRM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b13d4fb9-08c8-4514-a2cf-a5f74ead7ecc/IGVFFI4905TRRM.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep12_S348_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8287CDRW/",
"accession": "IGVFFI8287CDRW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:25:43.352029+00:00",
"file_format": "fastq",
"file_size": 905217,
"href": "/sequence-files/IGVFFI8287CDRW/@@download/IGVFFI8287CDRW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/719fbedb-5d85-4b78-a80b-1f427f5c0e76/IGVFFI8287CDRW.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep2_S248_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4035XOZM/",
"accession": "IGVFFI4035XOZM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:28:57.214343+00:00",
"file_format": "fastq",
"file_size": 818561,
"href": "/sequence-files/IGVFFI4035XOZM/@@download/IGVFFI4035XOZM.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep7_S343_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4590EFMQ/",
"accession": "IGVFFI4590EFMQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:26:10.960961+00:00",
"file_format": "fastq",
"file_size": 3705408,
"href": "/sequence-files/IGVFFI4590EFMQ/@@download/IGVFFI4590EFMQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bd5d42b7-b1db-42f7-88f4-e35303862926/IGVFFI4590EFMQ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep2_S248_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9854VTIE/",
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},
"submitted_files_timestamp": "2023-12-05T23:23:15.993255+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": "75974895-0210-49d1-8d31-8b7edc7379d4"
}