{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7083JDYN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7083JDYN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-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 [IGVFSM8031DKZT](/in-vitro-systems/IGVFSM8031DKZT/) 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/IGVFSM8031DKZT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8031DKZT](/in-vitro-systems/IGVFSM8031DKZT/) 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/IGVFSM8031DKZT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7083JDYN](/measurement-sets/IGVFDS7083JDYN/) 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/IGVFDS7083JDYN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7083JDYN](/measurement-sets/IGVFDS7083JDYN/) has sequence file(s) [IGVFFI9391BOEU](/sequence-files/IGVFFI9391BOEU/), [IGVFFI4300ZCKI](/sequence-files/IGVFFI4300ZCKI/), [IGVFFI1396GJZD](/sequence-files/IGVFFI1396GJZD/), [IGVFFI1753URQD](/sequence-files/IGVFFI1753URQD/), [IGVFFI8782QJTV](/sequence-files/IGVFFI8782QJTV/), [IGVFFI2754WFTD](/sequence-files/IGVFFI2754WFTD/), [IGVFFI2961OZIR](/sequence-files/IGVFFI2961OZIR/), [IGVFFI7635PWRP](/sequence-files/IGVFFI7635PWRP/), [IGVFFI0743TLOP](/sequence-files/IGVFFI0743TLOP/), [IGVFFI1841PHXH](/sequence-files/IGVFFI1841PHXH/), [IGVFFI1318JXAS](/sequence-files/IGVFFI1318JXAS/), [IGVFFI6756RIQB](/sequence-files/IGVFFI6756RIQB/), [IGVFFI8734TCNX](/sequence-files/IGVFFI8734TCNX/), [IGVFFI8488QDUB](/sequence-files/IGVFFI8488QDUB/), [IGVFFI3267RRIT](/sequence-files/IGVFFI3267RRIT/), [IGVFFI5575RSIB](/sequence-files/IGVFFI5575RSIB/), [IGVFFI8122QFXI](/sequence-files/IGVFFI8122QFXI/), [IGVFFI4990PBYD](/sequence-files/IGVFFI4990PBYD/), [IGVFFI2334KIJR](/sequence-files/IGVFFI2334KIJR/), [IGVFFI5665GVTB](/sequence-files/IGVFFI5665GVTB/), [IGVFFI4525YCKE](/sequence-files/IGVFFI4525YCKE/), [IGVFFI5712LFTX](/sequence-files/IGVFFI5712LFTX/), [IGVFFI8756HCNN](/sequence-files/IGVFFI8756HCNN/), [IGVFFI4386WZYI](/sequence-files/IGVFFI4386WZYI/), [IGVFFI9761VNNL](/sequence-files/IGVFFI9761VNNL/), [IGVFFI1408GFJL](/sequence-files/IGVFFI1408GFJL/), [IGVFFI8302OHMA](/sequence-files/IGVFFI8302OHMA/), [IGVFFI2630RBPQ](/sequence-files/IGVFFI2630RBPQ/), [IGVFFI5191RILC](/sequence-files/IGVFFI5191RILC/), [IGVFFI8900NJDW](/sequence-files/IGVFFI8900NJDW/), [IGVFFI6318PJER](/sequence-files/IGVFFI6318PJER/), [IGVFFI8369NAHH](/sequence-files/IGVFFI8369NAHH/), [IGVFFI8021JBTH](/sequence-files/IGVFFI8021JBTH/), [IGVFFI8335ZZPE](/sequence-files/IGVFFI8335ZZPE/), [IGVFFI0113QOIJ](/sequence-files/IGVFFI0113QOIJ/), [IGVFFI8630IZGF](/sequence-files/IGVFFI8630IZGF/), [IGVFFI3498LBMK](/sequence-files/IGVFFI3498LBMK/), [IGVFFI4604SVRJ](/sequence-files/IGVFFI4604SVRJ/), [IGVFFI8993KTTN](/sequence-files/IGVFFI8993KTTN/), [IGVFFI5252CUWH](/sequence-files/IGVFFI5252CUWH/), [IGVFFI6821JPKU](/sequence-files/IGVFFI6821JPKU/), [IGVFFI1107RGPC](/sequence-files/IGVFFI1107RGPC/), [IGVFFI9164DVFV](/sequence-files/IGVFFI9164DVFV/), [IGVFFI4236REUS](/sequence-files/IGVFFI4236REUS/), [IGVFFI1872UKWD](/sequence-files/IGVFFI1872UKWD/), [IGVFFI6436NPAE](/sequence-files/IGVFFI6436NPAE/), [IGVFFI4004FEZC](/sequence-files/IGVFFI4004FEZC/), [IGVFFI3522RNBI](/sequence-files/IGVFFI3522RNBI/) 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/IGVFDS7083JDYN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7083JDYN](/measurement-sets/IGVFDS7083JDYN/) has sequence file(s): [IGVFFI9391BOEU](/sequence-files/IGVFFI9391BOEU/), [IGVFFI4300ZCKI](/sequence-files/IGVFFI4300ZCKI/), [IGVFFI1396GJZD](/sequence-files/IGVFFI1396GJZD/), [IGVFFI1753URQD](/sequence-files/IGVFFI1753URQD/), [IGVFFI8782QJTV](/sequence-files/IGVFFI8782QJTV/), [IGVFFI2754WFTD](/sequence-files/IGVFFI2754WFTD/), [IGVFFI2961OZIR](/sequence-files/IGVFFI2961OZIR/), [IGVFFI7635PWRP](/sequence-files/IGVFFI7635PWRP/), [IGVFFI0743TLOP](/sequence-files/IGVFFI0743TLOP/), [IGVFFI1841PHXH](/sequence-files/IGVFFI1841PHXH/), [IGVFFI1318JXAS](/sequence-files/IGVFFI1318JXAS/), [IGVFFI6756RIQB](/sequence-files/IGVFFI6756RIQB/), [IGVFFI8734TCNX](/sequence-files/IGVFFI8734TCNX/), [IGVFFI8488QDUB](/sequence-files/IGVFFI8488QDUB/), [IGVFFI3267RRIT](/sequence-files/IGVFFI3267RRIT/), [IGVFFI5575RSIB](/sequence-files/IGVFFI5575RSIB/), [IGVFFI8122QFXI](/sequence-files/IGVFFI8122QFXI/), [IGVFFI4990PBYD](/sequence-files/IGVFFI4990PBYD/), [IGVFFI2334KIJR](/sequence-files/IGVFFI2334KIJR/), [IGVFFI5665GVTB](/sequence-files/IGVFFI5665GVTB/), [IGVFFI4525YCKE](/sequence-files/IGVFFI4525YCKE/), [IGVFFI5712LFTX](/sequence-files/IGVFFI5712LFTX/), [IGVFFI8756HCNN](/sequence-files/IGVFFI8756HCNN/), [IGVFFI4386WZYI](/sequence-files/IGVFFI4386WZYI/), [IGVFFI9761VNNL](/sequence-files/IGVFFI9761VNNL/), [IGVFFI1408GFJL](/sequence-files/IGVFFI1408GFJL/), [IGVFFI8302OHMA](/sequence-files/IGVFFI8302OHMA/), [IGVFFI2630RBPQ](/sequence-files/IGVFFI2630RBPQ/), [IGVFFI5191RILC](/sequence-files/IGVFFI5191RILC/), [IGVFFI8900NJDW](/sequence-files/IGVFFI8900NJDW/), [IGVFFI6318PJER](/sequence-files/IGVFFI6318PJER/), [IGVFFI8369NAHH](/sequence-files/IGVFFI8369NAHH/), [IGVFFI8021JBTH](/sequence-files/IGVFFI8021JBTH/), [IGVFFI8335ZZPE](/sequence-files/IGVFFI8335ZZPE/), [IGVFFI0113QOIJ](/sequence-files/IGVFFI0113QOIJ/), [IGVFFI8630IZGF](/sequence-files/IGVFFI8630IZGF/), [IGVFFI3498LBMK](/sequence-files/IGVFFI3498LBMK/), [IGVFFI4604SVRJ](/sequence-files/IGVFFI4604SVRJ/), [IGVFFI8993KTTN](/sequence-files/IGVFFI8993KTTN/), [IGVFFI5252CUWH](/sequence-files/IGVFFI5252CUWH/), [IGVFFI6821JPKU](/sequence-files/IGVFFI6821JPKU/), [IGVFFI1107RGPC](/sequence-files/IGVFFI1107RGPC/), [IGVFFI9164DVFV](/sequence-files/IGVFFI9164DVFV/), [IGVFFI4236REUS](/sequence-files/IGVFFI4236REUS/), [IGVFFI1872UKWD](/sequence-files/IGVFFI1872UKWD/), [IGVFFI6436NPAE](/sequence-files/IGVFFI6436NPAE/), [IGVFFI4004FEZC](/sequence-files/IGVFFI4004FEZC/), [IGVFFI3522RNBI](/sequence-files/IGVFFI3522RNBI/) 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/IGVFDS7083JDYN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7083JDYN](/measurement-sets/IGVFDS7083JDYN/) 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/IGVFDS7083JDYN/"
}
]
},
"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": "2023-11-30T22:48:56.713483+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/IGVFFI9391BOEU/",
"accession": "IGVFFI9391BOEU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep12_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:09:06.709390+00:00",
"file_format": "fastq",
"file_size": 7407604,
"href": "/sequence-files/IGVFFI9391BOEU/@@download/IGVFFI9391BOEU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d4444c13-7168-480d-a39c-a6171ceb82e2/IGVFFI9391BOEU.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-FFrep2-BinD-PCRrep12_S186_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4300ZCKI/",
"accession": "IGVFFI4300ZCKI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:13:02.130716+00:00",
"file_format": "fastq",
"file_size": 1638614,
"href": "/sequence-files/IGVFFI4300ZCKI/@@download/IGVFFI4300ZCKI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a320b8e4-89d7-4922-bd38-42b05847e51f/IGVFFI4300ZCKI.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-FFrep2-BinD-PCRrep8_S182_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1396GJZD/",
"accession": "IGVFFI1396GJZD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:39.325308+00:00",
"file_format": "fastq",
"file_size": 821084,
"href": "/sequence-files/IGVFFI1396GJZD/@@download/IGVFFI1396GJZD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2d11daf0-2228-4716-8e22-62014cdd7183/IGVFFI1396GJZD.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-BioRep1-FFrep2-BinD-PCRrep4_S88_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1753URQD/",
"accession": "IGVFFI1753URQD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep3_I2"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T20:10:02.430253+00:00",
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"file_size": 805344,
"href": "/sequence-files/IGVFFI1753URQD/@@download/IGVFFI1753URQD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/034cea9c-9ddd-4fdc-8e1e-cd65ebb371ad/IGVFFI1753URQD.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-FFrep2-BinD-PCRrep3_S87_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8782QJTV/",
"accession": "IGVFFI8782QJTV",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:11:53.147506+00:00",
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"href": "/sequence-files/IGVFFI8782QJTV/@@download/IGVFFI8782QJTV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ed118276-0c44-429c-bc0b-f2a9a2c940dc/IGVFFI8782QJTV.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-BioRep1-FFrep2-BinD-PCRrep6_S90_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2754WFTD/",
"accession": "IGVFFI2754WFTD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:57.523920+00:00",
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"file_size": 3848123,
"href": "/sequence-files/IGVFFI2754WFTD/@@download/IGVFFI2754WFTD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/33b6277a-16f1-4046-8ca4-8879c3e0205b/IGVFFI2754WFTD.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-BioRep1-FFrep2-BinD-PCRrep4_S88_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2961OZIR/",
"accession": "IGVFFI2961OZIR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:30.178192+00:00",
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"href": "/sequence-files/IGVFFI2961OZIR/@@download/IGVFFI2961OZIR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bb736190-7608-4b0a-a360-561fe0b55ffa/IGVFFI2961OZIR.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7635PWRP/",
"accession": "IGVFFI7635PWRP",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:11:06.684750+00:00",
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"href": "/sequence-files/IGVFFI7635PWRP/@@download/IGVFFI7635PWRP.fastq.gz",
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"status": "released",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0743TLOP/",
"accession": "IGVFFI0743TLOP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinD-PCRrep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:12:02.453217+00:00",
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"href": "/sequence-files/IGVFFI0743TLOP/@@download/IGVFFI0743TLOP.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-BioRep1-FFrep2-BinD-PCRrep6_S90_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1841PHXH/",
"accession": "IGVFFI1841PHXH",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:07:14.012923+00:00",
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"href": "/sequence-files/IGVFFI1841PHXH/@@download/IGVFFI1841PHXH.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 76-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:06:46.504915+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": "9d3027f8-c591-45ed-b943-1d9427a81794"
}