{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1285SAVV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1285SAVV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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 [IGVFSM3275SABA](/in-vitro-systems/IGVFSM3275SABA/) 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/IGVFSM3275SABA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3275SABA](/in-vitro-systems/IGVFSM3275SABA/) 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/IGVFSM3275SABA/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1285SAVV](/measurement-sets/IGVFDS1285SAVV/) 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/IGVFDS1285SAVV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1285SAVV](/measurement-sets/IGVFDS1285SAVV/) has sequence file(s) [IGVFFI6166IYEH](/sequence-files/IGVFFI6166IYEH/), [IGVFFI0506DBQH](/sequence-files/IGVFFI0506DBQH/), [IGVFFI5135ZACM](/sequence-files/IGVFFI5135ZACM/), [IGVFFI8677XRNK](/sequence-files/IGVFFI8677XRNK/), [IGVFFI7927FPTK](/sequence-files/IGVFFI7927FPTK/), [IGVFFI5087WSGS](/sequence-files/IGVFFI5087WSGS/), [IGVFFI9133SAYI](/sequence-files/IGVFFI9133SAYI/), [IGVFFI7089VBHS](/sequence-files/IGVFFI7089VBHS/), [IGVFFI2486NSVI](/sequence-files/IGVFFI2486NSVI/), [IGVFFI8112ZVPB](/sequence-files/IGVFFI8112ZVPB/), [IGVFFI7042MSRD](/sequence-files/IGVFFI7042MSRD/), [IGVFFI6463WXTK](/sequence-files/IGVFFI6463WXTK/), [IGVFFI0437BRJM](/sequence-files/IGVFFI0437BRJM/), [IGVFFI0135BHPL](/sequence-files/IGVFFI0135BHPL/), [IGVFFI6583JLOB](/sequence-files/IGVFFI6583JLOB/), [IGVFFI7752HDLQ](/sequence-files/IGVFFI7752HDLQ/), [IGVFFI0355DPZS](/sequence-files/IGVFFI0355DPZS/), [IGVFFI9208IUMP](/sequence-files/IGVFFI9208IUMP/), [IGVFFI5783LPLC](/sequence-files/IGVFFI5783LPLC/), [IGVFFI2684KLGM](/sequence-files/IGVFFI2684KLGM/), [IGVFFI4780QQPC](/sequence-files/IGVFFI4780QQPC/), [IGVFFI6774ICGQ](/sequence-files/IGVFFI6774ICGQ/), [IGVFFI8879PJJY](/sequence-files/IGVFFI8879PJJY/), [IGVFFI9264ISJO](/sequence-files/IGVFFI9264ISJO/), [IGVFFI2475CDEA](/sequence-files/IGVFFI2475CDEA/), [IGVFFI3170BSNL](/sequence-files/IGVFFI3170BSNL/), [IGVFFI0359GSBR](/sequence-files/IGVFFI0359GSBR/), [IGVFFI7556UYRP](/sequence-files/IGVFFI7556UYRP/), [IGVFFI2244FSQQ](/sequence-files/IGVFFI2244FSQQ/), [IGVFFI9677YSWT](/sequence-files/IGVFFI9677YSWT/), [IGVFFI4478UABJ](/sequence-files/IGVFFI4478UABJ/), [IGVFFI4078JPHG](/sequence-files/IGVFFI4078JPHG/), [IGVFFI5530DPTO](/sequence-files/IGVFFI5530DPTO/), [IGVFFI0603ZMUW](/sequence-files/IGVFFI0603ZMUW/), [IGVFFI8209ZGKG](/sequence-files/IGVFFI8209ZGKG/), [IGVFFI5880IRXW](/sequence-files/IGVFFI5880IRXW/), [IGVFFI1625GPWF](/sequence-files/IGVFFI1625GPWF/), [IGVFFI5120KWVL](/sequence-files/IGVFFI5120KWVL/), [IGVFFI2277YKXE](/sequence-files/IGVFFI2277YKXE/), [IGVFFI4532AJXD](/sequence-files/IGVFFI4532AJXD/), [IGVFFI6415IIIS](/sequence-files/IGVFFI6415IIIS/), [IGVFFI8888RUXR](/sequence-files/IGVFFI8888RUXR/), [IGVFFI5988PPUW](/sequence-files/IGVFFI5988PPUW/), [IGVFFI0402TMSY](/sequence-files/IGVFFI0402TMSY/), [IGVFFI6997SLOZ](/sequence-files/IGVFFI6997SLOZ/), [IGVFFI2319ZODY](/sequence-files/IGVFFI2319ZODY/), [IGVFFI5891EUZO](/sequence-files/IGVFFI5891EUZO/), [IGVFFI8943RRZF](/sequence-files/IGVFFI8943RRZF/) 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/IGVFDS1285SAVV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1285SAVV](/measurement-sets/IGVFDS1285SAVV/) has sequence file(s): [IGVFFI6166IYEH](/sequence-files/IGVFFI6166IYEH/), [IGVFFI0506DBQH](/sequence-files/IGVFFI0506DBQH/), [IGVFFI5135ZACM](/sequence-files/IGVFFI5135ZACM/), [IGVFFI8677XRNK](/sequence-files/IGVFFI8677XRNK/), [IGVFFI7927FPTK](/sequence-files/IGVFFI7927FPTK/), [IGVFFI5087WSGS](/sequence-files/IGVFFI5087WSGS/), [IGVFFI9133SAYI](/sequence-files/IGVFFI9133SAYI/), [IGVFFI7089VBHS](/sequence-files/IGVFFI7089VBHS/), [IGVFFI2486NSVI](/sequence-files/IGVFFI2486NSVI/), [IGVFFI8112ZVPB](/sequence-files/IGVFFI8112ZVPB/), [IGVFFI7042MSRD](/sequence-files/IGVFFI7042MSRD/), [IGVFFI6463WXTK](/sequence-files/IGVFFI6463WXTK/), [IGVFFI0437BRJM](/sequence-files/IGVFFI0437BRJM/), [IGVFFI0135BHPL](/sequence-files/IGVFFI0135BHPL/), [IGVFFI6583JLOB](/sequence-files/IGVFFI6583JLOB/), [IGVFFI7752HDLQ](/sequence-files/IGVFFI7752HDLQ/), [IGVFFI0355DPZS](/sequence-files/IGVFFI0355DPZS/), [IGVFFI9208IUMP](/sequence-files/IGVFFI9208IUMP/), [IGVFFI5783LPLC](/sequence-files/IGVFFI5783LPLC/), [IGVFFI2684KLGM](/sequence-files/IGVFFI2684KLGM/), [IGVFFI4780QQPC](/sequence-files/IGVFFI4780QQPC/), [IGVFFI6774ICGQ](/sequence-files/IGVFFI6774ICGQ/), [IGVFFI8879PJJY](/sequence-files/IGVFFI8879PJJY/), [IGVFFI9264ISJO](/sequence-files/IGVFFI9264ISJO/), [IGVFFI2475CDEA](/sequence-files/IGVFFI2475CDEA/), [IGVFFI3170BSNL](/sequence-files/IGVFFI3170BSNL/), [IGVFFI0359GSBR](/sequence-files/IGVFFI0359GSBR/), [IGVFFI7556UYRP](/sequence-files/IGVFFI7556UYRP/), [IGVFFI2244FSQQ](/sequence-files/IGVFFI2244FSQQ/), [IGVFFI9677YSWT](/sequence-files/IGVFFI9677YSWT/), [IGVFFI4478UABJ](/sequence-files/IGVFFI4478UABJ/), [IGVFFI4078JPHG](/sequence-files/IGVFFI4078JPHG/), [IGVFFI5530DPTO](/sequence-files/IGVFFI5530DPTO/), [IGVFFI0603ZMUW](/sequence-files/IGVFFI0603ZMUW/), [IGVFFI8209ZGKG](/sequence-files/IGVFFI8209ZGKG/), [IGVFFI5880IRXW](/sequence-files/IGVFFI5880IRXW/), [IGVFFI1625GPWF](/sequence-files/IGVFFI1625GPWF/), [IGVFFI5120KWVL](/sequence-files/IGVFFI5120KWVL/), [IGVFFI2277YKXE](/sequence-files/IGVFFI2277YKXE/), [IGVFFI4532AJXD](/sequence-files/IGVFFI4532AJXD/), [IGVFFI6415IIIS](/sequence-files/IGVFFI6415IIIS/), [IGVFFI8888RUXR](/sequence-files/IGVFFI8888RUXR/), [IGVFFI5988PPUW](/sequence-files/IGVFFI5988PPUW/), [IGVFFI0402TMSY](/sequence-files/IGVFFI0402TMSY/), [IGVFFI6997SLOZ](/sequence-files/IGVFFI6997SLOZ/), [IGVFFI2319ZODY](/sequence-files/IGVFFI2319ZODY/), [IGVFFI5891EUZO](/sequence-files/IGVFFI5891EUZO/), [IGVFFI8943RRZF](/sequence-files/IGVFFI8943RRZF/) 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/IGVFDS1285SAVV/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1285SAVV](/measurement-sets/IGVFDS1285SAVV/) 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/IGVFDS1285SAVV/"
}
]
},
"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": "2023-11-30T22:49:00.632408+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/IGVFFI6166IYEH/",
"accession": "IGVFFI6166IYEH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:07.873287+00:00",
"file_format": "fastq",
"file_size": 1538566,
"href": "/sequence-files/IGVFFI6166IYEH/@@download/IGVFFI6166IYEH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b0ad58d2-ae98-43c0-ab70-9685b3beb87e/IGVFFI6166IYEH.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-FFrep3-BinC-PCRrep7_S127_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0506DBQH/",
"accession": "IGVFFI0506DBQH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep9_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:37:31.371161+00:00",
"file_format": "fastq",
"file_size": 1459252,
"href": "/sequence-files/IGVFFI0506DBQH/@@download/IGVFFI0506DBQH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/24eb074f-0fa6-4cd7-a3be-64b67f0905ed/IGVFFI0506DBQH.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-FFrep3-BinC-PCRrep9_S129_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5135ZACM/",
"accession": "IGVFFI5135ZACM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:17.317495+00:00",
"file_format": "fastq",
"file_size": 1413087,
"href": "/sequence-files/IGVFFI5135ZACM/@@download/IGVFFI5135ZACM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7ab2f3b3-1f4e-4cdd-9aee-305cbd4be229/IGVFFI5135ZACM.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-FFrep3-BinC-PCRrep7_S127_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8677XRNK/",
"accession": "IGVFFI8677XRNK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:37:12.965486+00:00",
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"file_size": 7086242,
"href": "/sequence-files/IGVFFI8677XRNK/@@download/IGVFFI8677XRNK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/647227dd-8b18-447d-9a59-5b826fa9f68c/IGVFFI8677XRNK.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-FFrep3-BinC-PCRrep8_S128_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7927FPTK/",
"accession": "IGVFFI7927FPTK",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:32:34.936568+00:00",
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"file_size": 1264513,
"href": "/sequence-files/IGVFFI7927FPTK/@@download/IGVFFI7927FPTK.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-FFrep3-BinC-PCRrep12_S132_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5087WSGS/",
"accession": "IGVFFI5087WSGS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:33:39.671018+00:00",
"file_format": "fastq",
"file_size": 886233,
"href": "/sequence-files/IGVFFI5087WSGS/@@download/IGVFFI5087WSGS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8e3ded59-5eff-44f5-a857-b5a5b016b321/IGVFFI5087WSGS.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-FFrep3-BinC-PCRrep3_S33_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9133SAYI/",
"accession": "IGVFFI9133SAYI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep9_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:37:49.831386+00:00",
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"file_size": 6900056,
"href": "/sequence-files/IGVFFI9133SAYI/@@download/IGVFFI9133SAYI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/979aaf14-cb85-496e-815a-6e863ccfce71/IGVFFI9133SAYI.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7089VBHS/",
"accession": "IGVFFI7089VBHS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:35:30.825892+00:00",
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"file_size": 811379,
"href": "/sequence-files/IGVFFI7089VBHS/@@download/IGVFFI7089VBHS.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2486NSVI/",
"accession": "IGVFFI2486NSVI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinC-PCRrep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:36:26.546714+00:00",
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"file_size": 5259127,
"href": "/sequence-files/IGVFFI2486NSVI/@@download/IGVFFI2486NSVI.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/IGVFFI8112ZVPB/",
"accession": "IGVFFI8112ZVPB",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:35:40.084664+00:00",
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"file_size": 831804,
"href": "/sequence-files/IGVFFI8112ZVPB/@@download/IGVFFI8112ZVPB.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-FFrep3-BinC-PCRrep6_S36_I2_001.fastq.gz",
"upload_status": "validated"
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"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:30:34.526345+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": "9e03f5d5-8539-4eb2-bbef-81f030d785ff"
}