{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0621TDYK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0621TDYK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-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 [IGVFSM3264VOCP](/in-vitro-systems/IGVFSM3264VOCP/) 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/IGVFSM3264VOCP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3264VOCP](/in-vitro-systems/IGVFSM3264VOCP/) 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/IGVFSM3264VOCP/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0621TDYK](/measurement-sets/IGVFDS0621TDYK/) 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/IGVFDS0621TDYK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0621TDYK](/measurement-sets/IGVFDS0621TDYK/) has sequence file(s) [IGVFFI9651YFGG](/sequence-files/IGVFFI9651YFGG/), [IGVFFI0698GTIH](/sequence-files/IGVFFI0698GTIH/), [IGVFFI5930AYLY](/sequence-files/IGVFFI5930AYLY/), [IGVFFI7822LUBQ](/sequence-files/IGVFFI7822LUBQ/), [IGVFFI2527DBCS](/sequence-files/IGVFFI2527DBCS/), [IGVFFI0394WTJE](/sequence-files/IGVFFI0394WTJE/), [IGVFFI9890JLQX](/sequence-files/IGVFFI9890JLQX/), [IGVFFI9645BTMH](/sequence-files/IGVFFI9645BTMH/), [IGVFFI8505ZMCR](/sequence-files/IGVFFI8505ZMCR/), [IGVFFI0372VOOV](/sequence-files/IGVFFI0372VOOV/), [IGVFFI9227GJAS](/sequence-files/IGVFFI9227GJAS/), [IGVFFI8524OXGK](/sequence-files/IGVFFI8524OXGK/), [IGVFFI8672FJGM](/sequence-files/IGVFFI8672FJGM/), [IGVFFI4499DMSW](/sequence-files/IGVFFI4499DMSW/), [IGVFFI8099IKLL](/sequence-files/IGVFFI8099IKLL/), [IGVFFI6162CLIQ](/sequence-files/IGVFFI6162CLIQ/), [IGVFFI3740ZFUI](/sequence-files/IGVFFI3740ZFUI/), [IGVFFI0481USKB](/sequence-files/IGVFFI0481USKB/), [IGVFFI4605LBMF](/sequence-files/IGVFFI4605LBMF/), [IGVFFI7296FPVL](/sequence-files/IGVFFI7296FPVL/), [IGVFFI2164HHSW](/sequence-files/IGVFFI2164HHSW/), [IGVFFI0346XIJH](/sequence-files/IGVFFI0346XIJH/), [IGVFFI3241JEHX](/sequence-files/IGVFFI3241JEHX/), [IGVFFI9904KPHO](/sequence-files/IGVFFI9904KPHO/), [IGVFFI4970KHYZ](/sequence-files/IGVFFI4970KHYZ/), [IGVFFI9947DWOB](/sequence-files/IGVFFI9947DWOB/), [IGVFFI9549DAOG](/sequence-files/IGVFFI9549DAOG/), [IGVFFI9187WVNL](/sequence-files/IGVFFI9187WVNL/), [IGVFFI3111RZMZ](/sequence-files/IGVFFI3111RZMZ/), [IGVFFI4437FPJT](/sequence-files/IGVFFI4437FPJT/), [IGVFFI0840TFUH](/sequence-files/IGVFFI0840TFUH/), [IGVFFI6643KWMV](/sequence-files/IGVFFI6643KWMV/), [IGVFFI7346QUFM](/sequence-files/IGVFFI7346QUFM/), [IGVFFI2729JUTK](/sequence-files/IGVFFI2729JUTK/), [IGVFFI3268NBNX](/sequence-files/IGVFFI3268NBNX/), [IGVFFI9873JKPN](/sequence-files/IGVFFI9873JKPN/), [IGVFFI3608DOEV](/sequence-files/IGVFFI3608DOEV/), [IGVFFI3411JNEQ](/sequence-files/IGVFFI3411JNEQ/), [IGVFFI4021ZFJW](/sequence-files/IGVFFI4021ZFJW/), [IGVFFI1734SCAD](/sequence-files/IGVFFI1734SCAD/), [IGVFFI1422MCHI](/sequence-files/IGVFFI1422MCHI/), [IGVFFI6298IPGY](/sequence-files/IGVFFI6298IPGY/), [IGVFFI2749RFAT](/sequence-files/IGVFFI2749RFAT/), [IGVFFI3854NDPL](/sequence-files/IGVFFI3854NDPL/), [IGVFFI7017IDNO](/sequence-files/IGVFFI7017IDNO/), [IGVFFI9061JNFF](/sequence-files/IGVFFI9061JNFF/), [IGVFFI4011YQLR](/sequence-files/IGVFFI4011YQLR/), [IGVFFI8655NZXM](/sequence-files/IGVFFI8655NZXM/) 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/IGVFDS0621TDYK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0621TDYK](/measurement-sets/IGVFDS0621TDYK/) has sequence file(s): [IGVFFI9651YFGG](/sequence-files/IGVFFI9651YFGG/), [IGVFFI0698GTIH](/sequence-files/IGVFFI0698GTIH/), [IGVFFI5930AYLY](/sequence-files/IGVFFI5930AYLY/), [IGVFFI7822LUBQ](/sequence-files/IGVFFI7822LUBQ/), [IGVFFI2527DBCS](/sequence-files/IGVFFI2527DBCS/), [IGVFFI0394WTJE](/sequence-files/IGVFFI0394WTJE/), [IGVFFI9890JLQX](/sequence-files/IGVFFI9890JLQX/), [IGVFFI9645BTMH](/sequence-files/IGVFFI9645BTMH/), [IGVFFI8505ZMCR](/sequence-files/IGVFFI8505ZMCR/), [IGVFFI0372VOOV](/sequence-files/IGVFFI0372VOOV/), [IGVFFI9227GJAS](/sequence-files/IGVFFI9227GJAS/), [IGVFFI8524OXGK](/sequence-files/IGVFFI8524OXGK/), [IGVFFI8672FJGM](/sequence-files/IGVFFI8672FJGM/), [IGVFFI4499DMSW](/sequence-files/IGVFFI4499DMSW/), [IGVFFI8099IKLL](/sequence-files/IGVFFI8099IKLL/), [IGVFFI6162CLIQ](/sequence-files/IGVFFI6162CLIQ/), [IGVFFI3740ZFUI](/sequence-files/IGVFFI3740ZFUI/), [IGVFFI0481USKB](/sequence-files/IGVFFI0481USKB/), [IGVFFI4605LBMF](/sequence-files/IGVFFI4605LBMF/), [IGVFFI7296FPVL](/sequence-files/IGVFFI7296FPVL/), [IGVFFI2164HHSW](/sequence-files/IGVFFI2164HHSW/), [IGVFFI0346XIJH](/sequence-files/IGVFFI0346XIJH/), [IGVFFI3241JEHX](/sequence-files/IGVFFI3241JEHX/), [IGVFFI9904KPHO](/sequence-files/IGVFFI9904KPHO/), [IGVFFI4970KHYZ](/sequence-files/IGVFFI4970KHYZ/), [IGVFFI9947DWOB](/sequence-files/IGVFFI9947DWOB/), [IGVFFI9549DAOG](/sequence-files/IGVFFI9549DAOG/), [IGVFFI9187WVNL](/sequence-files/IGVFFI9187WVNL/), [IGVFFI3111RZMZ](/sequence-files/IGVFFI3111RZMZ/), [IGVFFI4437FPJT](/sequence-files/IGVFFI4437FPJT/), [IGVFFI0840TFUH](/sequence-files/IGVFFI0840TFUH/), [IGVFFI6643KWMV](/sequence-files/IGVFFI6643KWMV/), [IGVFFI7346QUFM](/sequence-files/IGVFFI7346QUFM/), [IGVFFI2729JUTK](/sequence-files/IGVFFI2729JUTK/), [IGVFFI3268NBNX](/sequence-files/IGVFFI3268NBNX/), [IGVFFI9873JKPN](/sequence-files/IGVFFI9873JKPN/), [IGVFFI3608DOEV](/sequence-files/IGVFFI3608DOEV/), [IGVFFI3411JNEQ](/sequence-files/IGVFFI3411JNEQ/), [IGVFFI4021ZFJW](/sequence-files/IGVFFI4021ZFJW/), [IGVFFI1734SCAD](/sequence-files/IGVFFI1734SCAD/), [IGVFFI1422MCHI](/sequence-files/IGVFFI1422MCHI/), [IGVFFI6298IPGY](/sequence-files/IGVFFI6298IPGY/), [IGVFFI2749RFAT](/sequence-files/IGVFFI2749RFAT/), [IGVFFI3854NDPL](/sequence-files/IGVFFI3854NDPL/), [IGVFFI7017IDNO](/sequence-files/IGVFFI7017IDNO/), [IGVFFI9061JNFF](/sequence-files/IGVFFI9061JNFF/), [IGVFFI4011YQLR](/sequence-files/IGVFFI4011YQLR/), [IGVFFI8655NZXM](/sequence-files/IGVFFI8655NZXM/) 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/IGVFDS0621TDYK/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0621TDYK](/measurement-sets/IGVFDS0621TDYK/) 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/IGVFDS0621TDYK/"
}
]
},
"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": "2023-11-30T22:49:06.173103+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/IGVFFI9651YFGG/",
"accession": "IGVFFI9651YFGG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:04:02.902220+00:00",
"file_format": "fastq",
"file_size": 877442,
"href": "/sequence-files/IGVFFI9651YFGG/@@download/IGVFFI9651YFGG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5390c3d6-4d94-402c-9bdc-c918509d3c06/IGVFFI9651YFGG.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-FFrep4-BinC-PCRrep2_S80_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0698GTIH/",
"accession": "IGVFFI0698GTIH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:04:12.219764+00:00",
"file_format": "fastq",
"file_size": 885281,
"href": "/sequence-files/IGVFFI0698GTIH/@@download/IGVFFI0698GTIH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1988398e-d7fc-46a0-83ba-d907cae2040f/IGVFFI0698GTIH.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-FFrep4-BinC-PCRrep2_S80_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5930AYLY/",
"accession": "IGVFFI5930AYLY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:07:28.038681+00:00",
"file_format": "fastq",
"file_size": 5138030,
"href": "/sequence-files/IGVFFI5930AYLY/@@download/IGVFFI5930AYLY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4ccf8352-1d47-4759-9ad5-bc4a3b164b24/IGVFFI5930AYLY.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-FFrep4-BinC-PCRrep7_S175_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7822LUBQ/",
"accession": "IGVFFI7822LUBQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep9_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:08:23.551418+00:00",
"file_format": "fastq",
"file_size": 1466400,
"href": "/sequence-files/IGVFFI7822LUBQ/@@download/IGVFFI7822LUBQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b9765ab2-d167-4b14-aa16-734a5f994a4d/IGVFFI7822LUBQ.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-FFrep4-BinC-PCRrep9_S177_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2527DBCS/",
"accession": "IGVFFI2527DBCS",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:07:00.156008+00:00",
"file_format": "fastq",
"file_size": 4049756,
"href": "/sequence-files/IGVFFI2527DBCS/@@download/IGVFFI2527DBCS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bff9a606-a9e9-4c7c-92ae-f7e289088572/IGVFFI2527DBCS.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-FFrep4-BinC-PCRrep6_S84_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0394WTJE/",
"accession": "IGVFFI0394WTJE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:01:33.351967+00:00",
"file_format": "fastq",
"file_size": 788793,
"href": "/sequence-files/IGVFFI0394WTJE/@@download/IGVFFI0394WTJE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8d030cde-b6b9-4979-b5b0-c11f82906e13/IGVFFI0394WTJE.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-FFrep4-BinC-PCRrep1_S79_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9890JLQX/",
"accession": "IGVFFI9890JLQX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:01:51.802462+00:00",
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"file_size": 3119381,
"href": "/sequence-files/IGVFFI9890JLQX/@@download/IGVFFI9890JLQX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fbda8a32-c10a-402d-90c0-76d944adce7b/IGVFFI9890JLQX.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9645BTMH/",
"accession": "IGVFFI9645BTMH",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:02:38.362857+00:00",
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"href": "/sequence-files/IGVFFI9645BTMH/@@download/IGVFFI9645BTMH.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8505ZMCR/",
"accession": "IGVFFI8505ZMCR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:08:14.332676+00:00",
"file_format": "fastq",
"file_size": 6787555,
"href": "/sequence-files/IGVFFI8505ZMCR/@@download/IGVFFI8505ZMCR.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-FFrep4-BinC-PCRrep8_S176_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0372VOOV/",
"accession": "IGVFFI0372VOOV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:07:18.616515+00:00",
"file_format": "fastq",
"file_size": 1400486,
"href": "/sequence-files/IGVFFI0372VOOV/@@download/IGVFFI0372VOOV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e3a7e058-6334-4b14-a49c-87a346d54023/IGVFFI0372VOOV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 51-75% 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": "2023-12-05T21:01:33.351967+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": "04821987-51be-4e95-b227-b89c921654a3"
}