{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1144XHLC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1144XHLC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM0040UFBQ](/in-vitro-systems/IGVFSM0040UFBQ/) 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/IGVFSM0040UFBQ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0040UFBQ](/in-vitro-systems/IGVFSM0040UFBQ/) 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/IGVFSM0040UFBQ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1144XHLC](/measurement-sets/IGVFDS1144XHLC/) 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/IGVFDS1144XHLC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1144XHLC](/measurement-sets/IGVFDS1144XHLC/) has sequence file(s) [IGVFFI0893PZWD](/sequence-files/IGVFFI0893PZWD/), [IGVFFI1786AGIJ](/sequence-files/IGVFFI1786AGIJ/), [IGVFFI0627NCQH](/sequence-files/IGVFFI0627NCQH/), [IGVFFI7593JPMV](/sequence-files/IGVFFI7593JPMV/), [IGVFFI0282WPLY](/sequence-files/IGVFFI0282WPLY/), [IGVFFI3090TLOC](/sequence-files/IGVFFI3090TLOC/), [IGVFFI2686JMAL](/sequence-files/IGVFFI2686JMAL/), [IGVFFI8408GZVT](/sequence-files/IGVFFI8408GZVT/), [IGVFFI9319NLLE](/sequence-files/IGVFFI9319NLLE/), [IGVFFI8264KXVR](/sequence-files/IGVFFI8264KXVR/), [IGVFFI1901OHTU](/sequence-files/IGVFFI1901OHTU/), [IGVFFI3367TFSD](/sequence-files/IGVFFI3367TFSD/), [IGVFFI2377JODR](/sequence-files/IGVFFI2377JODR/), [IGVFFI4863TVJF](/sequence-files/IGVFFI4863TVJF/), [IGVFFI6303BWPY](/sequence-files/IGVFFI6303BWPY/), [IGVFFI5309OLVN](/sequence-files/IGVFFI5309OLVN/), [IGVFFI6761RGRU](/sequence-files/IGVFFI6761RGRU/), [IGVFFI2780RGAA](/sequence-files/IGVFFI2780RGAA/), [IGVFFI2496YDNT](/sequence-files/IGVFFI2496YDNT/), [IGVFFI9549TEOP](/sequence-files/IGVFFI9549TEOP/), [IGVFFI1533MFML](/sequence-files/IGVFFI1533MFML/), [IGVFFI5378PFKN](/sequence-files/IGVFFI5378PFKN/), [IGVFFI1740DFEI](/sequence-files/IGVFFI1740DFEI/), [IGVFFI0504FXTN](/sequence-files/IGVFFI0504FXTN/), [IGVFFI3930XYCN](/sequence-files/IGVFFI3930XYCN/), [IGVFFI6679TFJG](/sequence-files/IGVFFI6679TFJG/), [IGVFFI8031MIZH](/sequence-files/IGVFFI8031MIZH/), [IGVFFI9456QPMY](/sequence-files/IGVFFI9456QPMY/), [IGVFFI7522LFNA](/sequence-files/IGVFFI7522LFNA/), [IGVFFI6480HCQM](/sequence-files/IGVFFI6480HCQM/), [IGVFFI0524KWWN](/sequence-files/IGVFFI0524KWWN/), [IGVFFI0341OVOB](/sequence-files/IGVFFI0341OVOB/), [IGVFFI6092TGAB](/sequence-files/IGVFFI6092TGAB/), [IGVFFI1219ASMM](/sequence-files/IGVFFI1219ASMM/), [IGVFFI1128ZEUF](/sequence-files/IGVFFI1128ZEUF/), [IGVFFI6887QKAR](/sequence-files/IGVFFI6887QKAR/), [IGVFFI1542BUMT](/sequence-files/IGVFFI1542BUMT/), [IGVFFI7004JPAK](/sequence-files/IGVFFI7004JPAK/), [IGVFFI7925BAKN](/sequence-files/IGVFFI7925BAKN/), [IGVFFI6497EPMA](/sequence-files/IGVFFI6497EPMA/), [IGVFFI2157SJGP](/sequence-files/IGVFFI2157SJGP/), [IGVFFI2566PPSW](/sequence-files/IGVFFI2566PPSW/), [IGVFFI3888GTEG](/sequence-files/IGVFFI3888GTEG/), [IGVFFI9506KMBF](/sequence-files/IGVFFI9506KMBF/), [IGVFFI4019NWEC](/sequence-files/IGVFFI4019NWEC/), [IGVFFI1689LWWH](/sequence-files/IGVFFI1689LWWH/), [IGVFFI5513SFLC](/sequence-files/IGVFFI5513SFLC/), [IGVFFI5859GVCS](/sequence-files/IGVFFI5859GVCS/) 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/IGVFDS1144XHLC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1144XHLC](/measurement-sets/IGVFDS1144XHLC/) has sequence file(s): [IGVFFI0893PZWD](/sequence-files/IGVFFI0893PZWD/), [IGVFFI1786AGIJ](/sequence-files/IGVFFI1786AGIJ/), [IGVFFI0627NCQH](/sequence-files/IGVFFI0627NCQH/), [IGVFFI7593JPMV](/sequence-files/IGVFFI7593JPMV/), [IGVFFI0282WPLY](/sequence-files/IGVFFI0282WPLY/), [IGVFFI3090TLOC](/sequence-files/IGVFFI3090TLOC/), [IGVFFI2686JMAL](/sequence-files/IGVFFI2686JMAL/), [IGVFFI8408GZVT](/sequence-files/IGVFFI8408GZVT/), [IGVFFI9319NLLE](/sequence-files/IGVFFI9319NLLE/), [IGVFFI8264KXVR](/sequence-files/IGVFFI8264KXVR/), [IGVFFI1901OHTU](/sequence-files/IGVFFI1901OHTU/), [IGVFFI3367TFSD](/sequence-files/IGVFFI3367TFSD/), [IGVFFI2377JODR](/sequence-files/IGVFFI2377JODR/), [IGVFFI4863TVJF](/sequence-files/IGVFFI4863TVJF/), [IGVFFI6303BWPY](/sequence-files/IGVFFI6303BWPY/), [IGVFFI5309OLVN](/sequence-files/IGVFFI5309OLVN/), [IGVFFI6761RGRU](/sequence-files/IGVFFI6761RGRU/), [IGVFFI2780RGAA](/sequence-files/IGVFFI2780RGAA/), [IGVFFI2496YDNT](/sequence-files/IGVFFI2496YDNT/), [IGVFFI9549TEOP](/sequence-files/IGVFFI9549TEOP/), [IGVFFI1533MFML](/sequence-files/IGVFFI1533MFML/), [IGVFFI5378PFKN](/sequence-files/IGVFFI5378PFKN/), [IGVFFI1740DFEI](/sequence-files/IGVFFI1740DFEI/), [IGVFFI0504FXTN](/sequence-files/IGVFFI0504FXTN/), [IGVFFI3930XYCN](/sequence-files/IGVFFI3930XYCN/), [IGVFFI6679TFJG](/sequence-files/IGVFFI6679TFJG/), [IGVFFI8031MIZH](/sequence-files/IGVFFI8031MIZH/), [IGVFFI9456QPMY](/sequence-files/IGVFFI9456QPMY/), [IGVFFI7522LFNA](/sequence-files/IGVFFI7522LFNA/), [IGVFFI6480HCQM](/sequence-files/IGVFFI6480HCQM/), [IGVFFI0524KWWN](/sequence-files/IGVFFI0524KWWN/), [IGVFFI0341OVOB](/sequence-files/IGVFFI0341OVOB/), [IGVFFI6092TGAB](/sequence-files/IGVFFI6092TGAB/), [IGVFFI1219ASMM](/sequence-files/IGVFFI1219ASMM/), [IGVFFI1128ZEUF](/sequence-files/IGVFFI1128ZEUF/), [IGVFFI6887QKAR](/sequence-files/IGVFFI6887QKAR/), [IGVFFI1542BUMT](/sequence-files/IGVFFI1542BUMT/), [IGVFFI7004JPAK](/sequence-files/IGVFFI7004JPAK/), [IGVFFI7925BAKN](/sequence-files/IGVFFI7925BAKN/), [IGVFFI6497EPMA](/sequence-files/IGVFFI6497EPMA/), [IGVFFI2157SJGP](/sequence-files/IGVFFI2157SJGP/), [IGVFFI2566PPSW](/sequence-files/IGVFFI2566PPSW/), [IGVFFI3888GTEG](/sequence-files/IGVFFI3888GTEG/), [IGVFFI9506KMBF](/sequence-files/IGVFFI9506KMBF/), [IGVFFI4019NWEC](/sequence-files/IGVFFI4019NWEC/), [IGVFFI1689LWWH](/sequence-files/IGVFFI1689LWWH/), [IGVFFI5513SFLC](/sequence-files/IGVFFI5513SFLC/), [IGVFFI5859GVCS](/sequence-files/IGVFFI5859GVCS/) 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/IGVFDS1144XHLC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1144XHLC](/measurement-sets/IGVFDS1144XHLC/) 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/IGVFDS1144XHLC/"
}
]
},
"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": "2023-11-30T22:48:52.992399+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/IGVFFI0893PZWD/",
"accession": "IGVFFI0893PZWD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:46:27.519074+00:00",
"file_format": "fastq",
"file_size": 3560611,
"href": "/sequence-files/IGVFFI0893PZWD/@@download/IGVFFI0893PZWD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6ebb8647-c3c5-4ef4-8f0c-c29a7e339653/IGVFFI0893PZWD.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-BinA-PCRrep3_S51_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1786AGIJ/",
"accession": "IGVFFI1786AGIJ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:48:37.820122+00:00",
"file_format": "fastq",
"file_size": 1616657,
"href": "/sequence-files/IGVFFI1786AGIJ/@@download/IGVFFI1786AGIJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a8305603-df15-4895-8a2e-6473ac4335f1/IGVFFI1786AGIJ.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-BinA-PCRrep7_S145_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0627NCQH/",
"accession": "IGVFFI0627NCQH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:50.629551+00:00",
"file_format": "fastq",
"file_size": 3338597,
"href": "/sequence-files/IGVFFI0627NCQH/@@download/IGVFFI0627NCQH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/664e12e2-690c-4c4a-b8b1-a84898e6508f/IGVFFI0627NCQH.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-BinA-PCRrep2_S50_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7593JPMV/",
"accession": "IGVFFI7593JPMV",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:44:36.386459+00:00",
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"file_size": 5039006,
"href": "/sequence-files/IGVFFI7593JPMV/@@download/IGVFFI7593JPMV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c0d52ab9-e868-45d3-a22a-c7767ad319ea/IGVFFI7593JPMV.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-BinA-PCRrep11_S149_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0282WPLY/",
"accession": "IGVFFI0282WPLY",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:47:42.057021+00:00",
"file_format": "fastq",
"file_size": 3463931,
"href": "/sequence-files/IGVFFI0282WPLY/@@download/IGVFFI0282WPLY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c805384b-216e-4b77-a915-b410d8d9a0d5/IGVFFI0282WPLY.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-BinA-PCRrep5_S53_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3090TLOC/",
"accession": "IGVFFI3090TLOC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:43:03.319730+00:00",
"file_format": "fastq",
"file_size": 926784,
"href": "/sequence-files/IGVFFI3090TLOC/@@download/IGVFFI3090TLOC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5934aac8-f090-4418-913e-cf31484c397d/IGVFFI3090TLOC.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-BinA-PCRrep1_S49_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2686JMAL/",
"accession": "IGVFFI2686JMAL",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:49:24.073153+00:00",
"file_format": "fastq",
"file_size": 1457843,
"href": "/sequence-files/IGVFFI2686JMAL/@@download/IGVFFI2686JMAL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4f4404ea-95de-4d1d-80b1-ddc312ed185b/IGVFFI2686JMAL.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8408GZVT/",
"accession": "IGVFFI8408GZVT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:59.945923+00:00",
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"href": "/sequence-files/IGVFFI8408GZVT/@@download/IGVFFI8408GZVT.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9319NLLE/",
"accession": "IGVFFI9319NLLE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:04.327755+00:00",
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"href": "/sequence-files/IGVFFI9319NLLE/@@download/IGVFFI9319NLLE.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-BinA-PCRrep12_S150_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8264KXVR/",
"accession": "IGVFFI8264KXVR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinA-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:46:09.235209+00:00",
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"file_size": 893529,
"href": "/sequence-files/IGVFFI8264KXVR/@@download/IGVFFI8264KXVR.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-BinA-PCRrep3_S51_I1_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": "2023-12-05T19:43:03.319730+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": "ca947d9f-6099-4a93-81c0-62ebe0f0ec8e"
}