{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2690TJJM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2690TJJM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-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 [IGVFSM2310CCFV](/in-vitro-systems/IGVFSM2310CCFV/) 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/IGVFSM2310CCFV/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2310CCFV](/in-vitro-systems/IGVFSM2310CCFV/) 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/IGVFSM2310CCFV/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2690TJJM](/measurement-sets/IGVFDS2690TJJM/) 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/IGVFDS2690TJJM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2690TJJM](/measurement-sets/IGVFDS2690TJJM/) has sequence file(s) [IGVFFI5415UEDE](/sequence-files/IGVFFI5415UEDE/), [IGVFFI0556IFKJ](/sequence-files/IGVFFI0556IFKJ/), [IGVFFI7108AVNK](/sequence-files/IGVFFI7108AVNK/), [IGVFFI1560JLCV](/sequence-files/IGVFFI1560JLCV/), [IGVFFI2379YFYC](/sequence-files/IGVFFI2379YFYC/), [IGVFFI4462AZJD](/sequence-files/IGVFFI4462AZJD/), [IGVFFI6882DUHO](/sequence-files/IGVFFI6882DUHO/), [IGVFFI7282SKON](/sequence-files/IGVFFI7282SKON/), [IGVFFI8337XJYA](/sequence-files/IGVFFI8337XJYA/), [IGVFFI4640DNSX](/sequence-files/IGVFFI4640DNSX/), [IGVFFI5516ESSK](/sequence-files/IGVFFI5516ESSK/), [IGVFFI9227RPDU](/sequence-files/IGVFFI9227RPDU/), [IGVFFI6079WMBN](/sequence-files/IGVFFI6079WMBN/), [IGVFFI1589OEAU](/sequence-files/IGVFFI1589OEAU/), [IGVFFI0019AJUY](/sequence-files/IGVFFI0019AJUY/), [IGVFFI9754KCQQ](/sequence-files/IGVFFI9754KCQQ/), [IGVFFI9489VDCE](/sequence-files/IGVFFI9489VDCE/), [IGVFFI2664LAQC](/sequence-files/IGVFFI2664LAQC/), [IGVFFI3384MZZZ](/sequence-files/IGVFFI3384MZZZ/), [IGVFFI8093EEJC](/sequence-files/IGVFFI8093EEJC/), [IGVFFI0251NPUZ](/sequence-files/IGVFFI0251NPUZ/), [IGVFFI5594MYYW](/sequence-files/IGVFFI5594MYYW/), [IGVFFI0628YAHP](/sequence-files/IGVFFI0628YAHP/), [IGVFFI8298ECSM](/sequence-files/IGVFFI8298ECSM/), [IGVFFI1977XIUI](/sequence-files/IGVFFI1977XIUI/), [IGVFFI5175GWLJ](/sequence-files/IGVFFI5175GWLJ/), [IGVFFI7960CKLM](/sequence-files/IGVFFI7960CKLM/), [IGVFFI4240NZLI](/sequence-files/IGVFFI4240NZLI/), [IGVFFI5882IBBB](/sequence-files/IGVFFI5882IBBB/), [IGVFFI8474QTEK](/sequence-files/IGVFFI8474QTEK/), [IGVFFI7532RIOK](/sequence-files/IGVFFI7532RIOK/), [IGVFFI5579JJTV](/sequence-files/IGVFFI5579JJTV/), [IGVFFI7980SIYV](/sequence-files/IGVFFI7980SIYV/), [IGVFFI5713FJEH](/sequence-files/IGVFFI5713FJEH/), [IGVFFI2612LBPZ](/sequence-files/IGVFFI2612LBPZ/), [IGVFFI8895CUNJ](/sequence-files/IGVFFI8895CUNJ/), [IGVFFI6433LVAD](/sequence-files/IGVFFI6433LVAD/), [IGVFFI6227XDXY](/sequence-files/IGVFFI6227XDXY/), [IGVFFI9008GSGG](/sequence-files/IGVFFI9008GSGG/), [IGVFFI1451FYYQ](/sequence-files/IGVFFI1451FYYQ/), [IGVFFI2913QILN](/sequence-files/IGVFFI2913QILN/), [IGVFFI5637OPON](/sequence-files/IGVFFI5637OPON/), [IGVFFI2225VINQ](/sequence-files/IGVFFI2225VINQ/), [IGVFFI8554OPUE](/sequence-files/IGVFFI8554OPUE/), [IGVFFI0945MRSC](/sequence-files/IGVFFI0945MRSC/), [IGVFFI7020USLV](/sequence-files/IGVFFI7020USLV/), [IGVFFI6277TIFA](/sequence-files/IGVFFI6277TIFA/), [IGVFFI4069UGKK](/sequence-files/IGVFFI4069UGKK/) 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/IGVFDS2690TJJM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2690TJJM](/measurement-sets/IGVFDS2690TJJM/) has sequence file(s): [IGVFFI5415UEDE](/sequence-files/IGVFFI5415UEDE/), [IGVFFI0556IFKJ](/sequence-files/IGVFFI0556IFKJ/), [IGVFFI7108AVNK](/sequence-files/IGVFFI7108AVNK/), [IGVFFI1560JLCV](/sequence-files/IGVFFI1560JLCV/), [IGVFFI2379YFYC](/sequence-files/IGVFFI2379YFYC/), [IGVFFI4462AZJD](/sequence-files/IGVFFI4462AZJD/), [IGVFFI6882DUHO](/sequence-files/IGVFFI6882DUHO/), [IGVFFI7282SKON](/sequence-files/IGVFFI7282SKON/), [IGVFFI8337XJYA](/sequence-files/IGVFFI8337XJYA/), [IGVFFI4640DNSX](/sequence-files/IGVFFI4640DNSX/), [IGVFFI5516ESSK](/sequence-files/IGVFFI5516ESSK/), [IGVFFI9227RPDU](/sequence-files/IGVFFI9227RPDU/), [IGVFFI6079WMBN](/sequence-files/IGVFFI6079WMBN/), [IGVFFI1589OEAU](/sequence-files/IGVFFI1589OEAU/), [IGVFFI0019AJUY](/sequence-files/IGVFFI0019AJUY/), [IGVFFI9754KCQQ](/sequence-files/IGVFFI9754KCQQ/), [IGVFFI9489VDCE](/sequence-files/IGVFFI9489VDCE/), [IGVFFI2664LAQC](/sequence-files/IGVFFI2664LAQC/), [IGVFFI3384MZZZ](/sequence-files/IGVFFI3384MZZZ/), [IGVFFI8093EEJC](/sequence-files/IGVFFI8093EEJC/), [IGVFFI0251NPUZ](/sequence-files/IGVFFI0251NPUZ/), [IGVFFI5594MYYW](/sequence-files/IGVFFI5594MYYW/), [IGVFFI0628YAHP](/sequence-files/IGVFFI0628YAHP/), [IGVFFI8298ECSM](/sequence-files/IGVFFI8298ECSM/), [IGVFFI1977XIUI](/sequence-files/IGVFFI1977XIUI/), [IGVFFI5175GWLJ](/sequence-files/IGVFFI5175GWLJ/), [IGVFFI7960CKLM](/sequence-files/IGVFFI7960CKLM/), [IGVFFI4240NZLI](/sequence-files/IGVFFI4240NZLI/), [IGVFFI5882IBBB](/sequence-files/IGVFFI5882IBBB/), [IGVFFI8474QTEK](/sequence-files/IGVFFI8474QTEK/), [IGVFFI7532RIOK](/sequence-files/IGVFFI7532RIOK/), [IGVFFI5579JJTV](/sequence-files/IGVFFI5579JJTV/), [IGVFFI7980SIYV](/sequence-files/IGVFFI7980SIYV/), [IGVFFI5713FJEH](/sequence-files/IGVFFI5713FJEH/), [IGVFFI2612LBPZ](/sequence-files/IGVFFI2612LBPZ/), [IGVFFI8895CUNJ](/sequence-files/IGVFFI8895CUNJ/), [IGVFFI6433LVAD](/sequence-files/IGVFFI6433LVAD/), [IGVFFI6227XDXY](/sequence-files/IGVFFI6227XDXY/), [IGVFFI9008GSGG](/sequence-files/IGVFFI9008GSGG/), [IGVFFI1451FYYQ](/sequence-files/IGVFFI1451FYYQ/), [IGVFFI2913QILN](/sequence-files/IGVFFI2913QILN/), [IGVFFI5637OPON](/sequence-files/IGVFFI5637OPON/), [IGVFFI2225VINQ](/sequence-files/IGVFFI2225VINQ/), [IGVFFI8554OPUE](/sequence-files/IGVFFI8554OPUE/), [IGVFFI0945MRSC](/sequence-files/IGVFFI0945MRSC/), [IGVFFI7020USLV](/sequence-files/IGVFFI7020USLV/), [IGVFFI6277TIFA](/sequence-files/IGVFFI6277TIFA/), [IGVFFI4069UGKK](/sequence-files/IGVFFI4069UGKK/) 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/IGVFDS2690TJJM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2690TJJM](/measurement-sets/IGVFDS2690TJJM/) 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/IGVFDS2690TJJM/"
}
]
},
"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": "2023-11-30T22:49:28.833568+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/IGVFFI5415UEDE/",
"accession": "IGVFFI5415UEDE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep10_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:47:49.023849+00:00",
"file_format": "fastq",
"file_size": 3608953,
"href": "/sequence-files/IGVFFI5415UEDE/@@download/IGVFFI5415UEDE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d4001fd7-3a93-4c63-acba-1a349f2c22fc/IGVFFI5415UEDE.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-BinD-PCRrep10_S382_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0556IFKJ/",
"accession": "IGVFFI0556IFKJ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:49:20.740870+00:00",
"file_format": "fastq",
"file_size": 887067,
"href": "/sequence-files/IGVFFI0556IFKJ/@@download/IGVFFI0556IFKJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/90af0aa7-9470-4292-b69b-432040f631f4/IGVFFI0556IFKJ.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-BinD-PCRrep2_S284_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7108AVNK/",
"accession": "IGVFFI7108AVNK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:50:43.305679+00:00",
"file_format": "fastq",
"file_size": 3220357,
"href": "/sequence-files/IGVFFI7108AVNK/@@download/IGVFFI7108AVNK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2698b049-3c74-404a-ba47-682fd0b1fe5c/IGVFFI7108AVNK.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-BinD-PCRrep4_S286_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1560JLCV/",
"accession": "IGVFFI1560JLCV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:50:06.509046+00:00",
"file_format": "fastq",
"file_size": 3203222,
"href": "/sequence-files/IGVFFI1560JLCV/@@download/IGVFFI1560JLCV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/430e0887-b9b7-4629-a525-dc8fb36460d2/IGVFFI1560JLCV.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-BinD-PCRrep3_S285_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2379YFYC/",
"accession": "IGVFFI2379YFYC",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:53:28.555125+00:00",
"file_format": "fastq",
"file_size": 886074,
"href": "/sequence-files/IGVFFI2379YFYC/@@download/IGVFFI2379YFYC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2d70c46a-a2ec-4a38-a573-19bb25b7312e/IGVFFI2379YFYC.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-BinD-PCRrep9_S381_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4462AZJD/",
"accession": "IGVFFI4462AZJD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:53:01.043684+00:00",
"file_format": "fastq",
"file_size": 870754,
"href": "/sequence-files/IGVFFI4462AZJD/@@download/IGVFFI4462AZJD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/89a19000-353f-4bfc-9a88-a113e1bf78e9/IGVFFI4462AZJD.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-BinD-PCRrep8_S380_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6882DUHO/",
"accession": "IGVFFI6882DUHO",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:50:15.701021+00:00",
"file_format": "fastq",
"file_size": 3827268,
"href": "/sequence-files/IGVFFI6882DUHO/@@download/IGVFFI6882DUHO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5a7ddb60-e670-41b1-933b-ba7bd3be282a/IGVFFI6882DUHO.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7282SKON/",
"accession": "IGVFFI7282SKON",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:51:47.592491+00:00",
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"file_size": 811244,
"href": "/sequence-files/IGVFFI7282SKON/@@download/IGVFFI7282SKON.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-BinD-PCRrep6_S288_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8337XJYA/",
"accession": "IGVFFI8337XJYA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep11_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:48:07.274997+00:00",
"file_format": "fastq",
"file_size": 806781,
"href": "/sequence-files/IGVFFI8337XJYA/@@download/IGVFFI8337XJYA.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-BinD-PCRrep11_S383_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4640DNSX/",
"accession": "IGVFFI4640DNSX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:52:24.380406+00:00",
"file_format": "fastq",
"file_size": 820836,
"href": "/sequence-files/IGVFFI4640DNSX/@@download/IGVFFI4640DNSX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6a1aa394-1c6a-46dd-a7f5-2a9da374681d/IGVFFI4640DNSX.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-BinD-PCRrep7_S379_I2_001.fastq.gz",
"upload_status": "validated"
},
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},
"submitted_files_timestamp": "2023-12-05T23:46:44.483431+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": "4e61fb64-f131-490e-bcc4-5ca0a2ed11f9"
}