{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5405RYGU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5405RYGU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-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 [IGVFSM6331RKYX](/in-vitro-systems/IGVFSM6331RKYX/) 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/IGVFSM6331RKYX/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6331RKYX](/in-vitro-systems/IGVFSM6331RKYX/) 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/IGVFSM6331RKYX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5405RYGU](/measurement-sets/IGVFDS5405RYGU/) 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/IGVFDS5405RYGU/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5405RYGU](/measurement-sets/IGVFDS5405RYGU/) has sequence file(s) [IGVFFI5920LYEU](/sequence-files/IGVFFI5920LYEU/), [IGVFFI8687AKIE](/sequence-files/IGVFFI8687AKIE/), [IGVFFI8602XCBR](/sequence-files/IGVFFI8602XCBR/), [IGVFFI6588TAXD](/sequence-files/IGVFFI6588TAXD/), [IGVFFI7579EAPB](/sequence-files/IGVFFI7579EAPB/), [IGVFFI4292LYJU](/sequence-files/IGVFFI4292LYJU/), [IGVFFI1958UOUF](/sequence-files/IGVFFI1958UOUF/), [IGVFFI2792QYHQ](/sequence-files/IGVFFI2792QYHQ/), [IGVFFI0219LPMU](/sequence-files/IGVFFI0219LPMU/), [IGVFFI3408LAGR](/sequence-files/IGVFFI3408LAGR/), [IGVFFI3667ASMR](/sequence-files/IGVFFI3667ASMR/), [IGVFFI0553UBWG](/sequence-files/IGVFFI0553UBWG/), [IGVFFI8799ZDJS](/sequence-files/IGVFFI8799ZDJS/), [IGVFFI3849YHMD](/sequence-files/IGVFFI3849YHMD/), [IGVFFI1287CKNT](/sequence-files/IGVFFI1287CKNT/), [IGVFFI6094UFWL](/sequence-files/IGVFFI6094UFWL/), [IGVFFI3614BVAY](/sequence-files/IGVFFI3614BVAY/), [IGVFFI6214KLPO](/sequence-files/IGVFFI6214KLPO/), [IGVFFI4509QWNW](/sequence-files/IGVFFI4509QWNW/), [IGVFFI8544SSHH](/sequence-files/IGVFFI8544SSHH/), [IGVFFI4636QHGS](/sequence-files/IGVFFI4636QHGS/), [IGVFFI3742YENH](/sequence-files/IGVFFI3742YENH/), [IGVFFI8573LNOD](/sequence-files/IGVFFI8573LNOD/), [IGVFFI6493OGUO](/sequence-files/IGVFFI6493OGUO/), [IGVFFI5865YWJA](/sequence-files/IGVFFI5865YWJA/), [IGVFFI9085EHXI](/sequence-files/IGVFFI9085EHXI/), [IGVFFI2981MOWH](/sequence-files/IGVFFI2981MOWH/), [IGVFFI7973WACJ](/sequence-files/IGVFFI7973WACJ/), [IGVFFI3437WHNQ](/sequence-files/IGVFFI3437WHNQ/), [IGVFFI7003KKNC](/sequence-files/IGVFFI7003KKNC/), [IGVFFI8179KVKI](/sequence-files/IGVFFI8179KVKI/), [IGVFFI5849LHNQ](/sequence-files/IGVFFI5849LHNQ/), [IGVFFI6351LQJK](/sequence-files/IGVFFI6351LQJK/), [IGVFFI4748HJGK](/sequence-files/IGVFFI4748HJGK/), [IGVFFI4425ZZGW](/sequence-files/IGVFFI4425ZZGW/), [IGVFFI1887INXT](/sequence-files/IGVFFI1887INXT/), [IGVFFI1769RTVV](/sequence-files/IGVFFI1769RTVV/), [IGVFFI6684RYQW](/sequence-files/IGVFFI6684RYQW/), [IGVFFI9793IGUJ](/sequence-files/IGVFFI9793IGUJ/), [IGVFFI0898KSJR](/sequence-files/IGVFFI0898KSJR/), [IGVFFI6879VNXZ](/sequence-files/IGVFFI6879VNXZ/), [IGVFFI4189OREP](/sequence-files/IGVFFI4189OREP/), [IGVFFI3611YEOE](/sequence-files/IGVFFI3611YEOE/), [IGVFFI5361ZAGU](/sequence-files/IGVFFI5361ZAGU/), [IGVFFI5084POXE](/sequence-files/IGVFFI5084POXE/), [IGVFFI0583XHMV](/sequence-files/IGVFFI0583XHMV/), [IGVFFI1854KRJY](/sequence-files/IGVFFI1854KRJY/), [IGVFFI0267EBZW](/sequence-files/IGVFFI0267EBZW/) 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/IGVFDS5405RYGU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5405RYGU](/measurement-sets/IGVFDS5405RYGU/) has sequence file(s): [IGVFFI5920LYEU](/sequence-files/IGVFFI5920LYEU/), [IGVFFI8687AKIE](/sequence-files/IGVFFI8687AKIE/), [IGVFFI8602XCBR](/sequence-files/IGVFFI8602XCBR/), [IGVFFI6588TAXD](/sequence-files/IGVFFI6588TAXD/), [IGVFFI7579EAPB](/sequence-files/IGVFFI7579EAPB/), [IGVFFI4292LYJU](/sequence-files/IGVFFI4292LYJU/), [IGVFFI1958UOUF](/sequence-files/IGVFFI1958UOUF/), [IGVFFI2792QYHQ](/sequence-files/IGVFFI2792QYHQ/), [IGVFFI0219LPMU](/sequence-files/IGVFFI0219LPMU/), [IGVFFI3408LAGR](/sequence-files/IGVFFI3408LAGR/), [IGVFFI3667ASMR](/sequence-files/IGVFFI3667ASMR/), [IGVFFI0553UBWG](/sequence-files/IGVFFI0553UBWG/), [IGVFFI8799ZDJS](/sequence-files/IGVFFI8799ZDJS/), [IGVFFI3849YHMD](/sequence-files/IGVFFI3849YHMD/), [IGVFFI1287CKNT](/sequence-files/IGVFFI1287CKNT/), [IGVFFI6094UFWL](/sequence-files/IGVFFI6094UFWL/), [IGVFFI3614BVAY](/sequence-files/IGVFFI3614BVAY/), [IGVFFI6214KLPO](/sequence-files/IGVFFI6214KLPO/), [IGVFFI4509QWNW](/sequence-files/IGVFFI4509QWNW/), [IGVFFI8544SSHH](/sequence-files/IGVFFI8544SSHH/), [IGVFFI4636QHGS](/sequence-files/IGVFFI4636QHGS/), [IGVFFI3742YENH](/sequence-files/IGVFFI3742YENH/), [IGVFFI8573LNOD](/sequence-files/IGVFFI8573LNOD/), [IGVFFI6493OGUO](/sequence-files/IGVFFI6493OGUO/), [IGVFFI5865YWJA](/sequence-files/IGVFFI5865YWJA/), [IGVFFI9085EHXI](/sequence-files/IGVFFI9085EHXI/), [IGVFFI2981MOWH](/sequence-files/IGVFFI2981MOWH/), [IGVFFI7973WACJ](/sequence-files/IGVFFI7973WACJ/), [IGVFFI3437WHNQ](/sequence-files/IGVFFI3437WHNQ/), [IGVFFI7003KKNC](/sequence-files/IGVFFI7003KKNC/), [IGVFFI8179KVKI](/sequence-files/IGVFFI8179KVKI/), [IGVFFI5849LHNQ](/sequence-files/IGVFFI5849LHNQ/), [IGVFFI6351LQJK](/sequence-files/IGVFFI6351LQJK/), [IGVFFI4748HJGK](/sequence-files/IGVFFI4748HJGK/), [IGVFFI4425ZZGW](/sequence-files/IGVFFI4425ZZGW/), [IGVFFI1887INXT](/sequence-files/IGVFFI1887INXT/), [IGVFFI1769RTVV](/sequence-files/IGVFFI1769RTVV/), [IGVFFI6684RYQW](/sequence-files/IGVFFI6684RYQW/), [IGVFFI9793IGUJ](/sequence-files/IGVFFI9793IGUJ/), [IGVFFI0898KSJR](/sequence-files/IGVFFI0898KSJR/), [IGVFFI6879VNXZ](/sequence-files/IGVFFI6879VNXZ/), [IGVFFI4189OREP](/sequence-files/IGVFFI4189OREP/), [IGVFFI3611YEOE](/sequence-files/IGVFFI3611YEOE/), [IGVFFI5361ZAGU](/sequence-files/IGVFFI5361ZAGU/), [IGVFFI5084POXE](/sequence-files/IGVFFI5084POXE/), [IGVFFI0583XHMV](/sequence-files/IGVFFI0583XHMV/), [IGVFFI1854KRJY](/sequence-files/IGVFFI1854KRJY/), [IGVFFI0267EBZW](/sequence-files/IGVFFI0267EBZW/) 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/IGVFDS5405RYGU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5405RYGU](/measurement-sets/IGVFDS5405RYGU/) 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/IGVFDS5405RYGU/"
}
]
},
"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": "2023-12-01T00:04:45.584078+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/IGVFFI5920LYEU/",
"accession": "IGVFFI5920LYEU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:39.347171+00:00",
"file_format": "fastq",
"file_size": 918968,
"href": "/sequence-files/IGVFFI5920LYEU/@@download/IGVFFI5920LYEU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c1b48506-f1a9-4556-af0a-0439eab363ed/IGVFFI5920LYEU.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-FFrep1-BinD-PCRrep2_S38_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8687AKIE/",
"accession": "IGVFFI8687AKIE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:39:21.261521+00:00",
"file_format": "fastq",
"file_size": 1613248,
"href": "/sequence-files/IGVFFI8687AKIE/@@download/IGVFFI8687AKIE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/aabab5d9-86c8-4ad6-852c-4264273d26db/IGVFFI8687AKIE.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-FFrep1-BinD-PCRrep8_S134_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8602XCBR/",
"accession": "IGVFFI8602XCBR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:38:44.323560+00:00",
"file_format": "fastq",
"file_size": 1705654,
"href": "/sequence-files/IGVFFI8602XCBR/@@download/IGVFFI8602XCBR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/41386f48-79a0-4901-a50a-a524bd7acbd9/IGVFFI8602XCBR.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-FFrep1-BinD-PCRrep7_S133_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6588TAXD/",
"accession": "IGVFFI6588TAXD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:38:25.810661+00:00",
"file_format": "fastq",
"file_size": 3481075,
"href": "/sequence-files/IGVFFI6588TAXD/@@download/IGVFFI6588TAXD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ce5c70bc-6f39-4f03-a821-a4cbeea45922/IGVFFI6588TAXD.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-FFrep1-BinD-PCRrep6_S42_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7579EAPB/",
"accession": "IGVFFI7579EAPB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:53.694987+00:00",
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"file_size": 855694,
"href": "/sequence-files/IGVFFI7579EAPB/@@download/IGVFFI7579EAPB.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-FFrep1-BinD-PCRrep4_S40_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4292LYJU/",
"accession": "IGVFFI4292LYJU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:35.019169+00:00",
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"file_size": 3723219,
"href": "/sequence-files/IGVFFI4292LYJU/@@download/IGVFFI4292LYJU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9c8617f2-738d-44c7-95af-36c091ca7ca8/IGVFFI4292LYJU.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-FFrep1-BinD-PCRrep3_S39_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1958UOUF/",
"accession": "IGVFFI1958UOUF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:37:30.567167+00:00",
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"href": "/sequence-files/IGVFFI1958UOUF/@@download/IGVFFI1958UOUF.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep5_S41_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2792QYHQ/",
"accession": "IGVFFI2792QYHQ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:40:26.470967+00:00",
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"href": "/sequence-files/IGVFFI2792QYHQ/@@download/IGVFFI2792QYHQ.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0219LPMU/",
"accession": "IGVFFI0219LPMU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:37:02.842169+00:00",
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"file_size": 865050,
"href": "/sequence-files/IGVFFI0219LPMU/@@download/IGVFFI0219LPMU.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-FFrep1-BinD-PCRrep4_S40_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3408LAGR/",
"accession": "IGVFFI3408LAGR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinD-PCRrep5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:37:58.092975+00:00",
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"href": "/sequence-files/IGVFFI3408LAGR/@@download/IGVFFI3408LAGR.fastq.gz",
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"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"status": "released",
"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": "2023-12-05T19:33:06.388762+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": "f016c775-b215-4660-b119-5a7f3b736144"
}