{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9665GYVE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9665GYVE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-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": "missing publication",
"detail": "Measurement set [IGVFDS9665GYVE](/measurement-sets/IGVFDS9665GYVE/) 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/IGVFDS9665GYVE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9665GYVE](/measurement-sets/IGVFDS9665GYVE/) has sequence file(s) [IGVFFI0230OXLP](/sequence-files/IGVFFI0230OXLP/), [IGVFFI9575KRZR](/sequence-files/IGVFFI9575KRZR/), [IGVFFI5023RDPK](/sequence-files/IGVFFI5023RDPK/), [IGVFFI5868MZNY](/sequence-files/IGVFFI5868MZNY/), [IGVFFI2937OMXA](/sequence-files/IGVFFI2937OMXA/), [IGVFFI5900PBEK](/sequence-files/IGVFFI5900PBEK/), [IGVFFI0503EQVR](/sequence-files/IGVFFI0503EQVR/), [IGVFFI3119HSES](/sequence-files/IGVFFI3119HSES/), [IGVFFI5806CXVA](/sequence-files/IGVFFI5806CXVA/), [IGVFFI8088FUDW](/sequence-files/IGVFFI8088FUDW/), [IGVFFI5944KRHZ](/sequence-files/IGVFFI5944KRHZ/), [IGVFFI9302KDEB](/sequence-files/IGVFFI9302KDEB/), [IGVFFI9275ZMNQ](/sequence-files/IGVFFI9275ZMNQ/), [IGVFFI2939VUID](/sequence-files/IGVFFI2939VUID/), [IGVFFI4712WWMO](/sequence-files/IGVFFI4712WWMO/), [IGVFFI6220CJJS](/sequence-files/IGVFFI6220CJJS/), [IGVFFI4151HPPC](/sequence-files/IGVFFI4151HPPC/), [IGVFFI0917YRJC](/sequence-files/IGVFFI0917YRJC/), [IGVFFI1321DUBS](/sequence-files/IGVFFI1321DUBS/), [IGVFFI5992XUCU](/sequence-files/IGVFFI5992XUCU/), [IGVFFI5429KGUP](/sequence-files/IGVFFI5429KGUP/), [IGVFFI3642IOQG](/sequence-files/IGVFFI3642IOQG/), [IGVFFI6182DUUK](/sequence-files/IGVFFI6182DUUK/), [IGVFFI2167SQMA](/sequence-files/IGVFFI2167SQMA/), [IGVFFI6897VGAO](/sequence-files/IGVFFI6897VGAO/), [IGVFFI0296RHNQ](/sequence-files/IGVFFI0296RHNQ/), [IGVFFI3092RSYJ](/sequence-files/IGVFFI3092RSYJ/), [IGVFFI3359MYGY](/sequence-files/IGVFFI3359MYGY/), [IGVFFI4429FTBT](/sequence-files/IGVFFI4429FTBT/), [IGVFFI6932JMTL](/sequence-files/IGVFFI6932JMTL/), [IGVFFI0832ELWX](/sequence-files/IGVFFI0832ELWX/), [IGVFFI8978FICD](/sequence-files/IGVFFI8978FICD/), [IGVFFI5604YDMA](/sequence-files/IGVFFI5604YDMA/), [IGVFFI9895VNQK](/sequence-files/IGVFFI9895VNQK/), [IGVFFI8209ZUHX](/sequence-files/IGVFFI8209ZUHX/), [IGVFFI5531NSKH](/sequence-files/IGVFFI5531NSKH/), [IGVFFI4594GEMX](/sequence-files/IGVFFI4594GEMX/), [IGVFFI1696NEGU](/sequence-files/IGVFFI1696NEGU/), [IGVFFI3578CLFN](/sequence-files/IGVFFI3578CLFN/), [IGVFFI3070RHFT](/sequence-files/IGVFFI3070RHFT/), [IGVFFI0286LFLQ](/sequence-files/IGVFFI0286LFLQ/), [IGVFFI0292BVKK](/sequence-files/IGVFFI0292BVKK/), [IGVFFI5186PSYN](/sequence-files/IGVFFI5186PSYN/), [IGVFFI6400DTKK](/sequence-files/IGVFFI6400DTKK/), [IGVFFI4858HNCG](/sequence-files/IGVFFI4858HNCG/), [IGVFFI8127GGZP](/sequence-files/IGVFFI8127GGZP/), [IGVFFI2400PGDF](/sequence-files/IGVFFI2400PGDF/), [IGVFFI5464FKHL](/sequence-files/IGVFFI5464FKHL/) 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/IGVFDS9665GYVE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9665GYVE](/measurement-sets/IGVFDS9665GYVE/) has sequence file(s): [IGVFFI0230OXLP](/sequence-files/IGVFFI0230OXLP/), [IGVFFI9575KRZR](/sequence-files/IGVFFI9575KRZR/), [IGVFFI5023RDPK](/sequence-files/IGVFFI5023RDPK/), [IGVFFI5868MZNY](/sequence-files/IGVFFI5868MZNY/), [IGVFFI2937OMXA](/sequence-files/IGVFFI2937OMXA/), [IGVFFI5900PBEK](/sequence-files/IGVFFI5900PBEK/), [IGVFFI0503EQVR](/sequence-files/IGVFFI0503EQVR/), [IGVFFI3119HSES](/sequence-files/IGVFFI3119HSES/), [IGVFFI5806CXVA](/sequence-files/IGVFFI5806CXVA/), [IGVFFI8088FUDW](/sequence-files/IGVFFI8088FUDW/), [IGVFFI5944KRHZ](/sequence-files/IGVFFI5944KRHZ/), [IGVFFI9302KDEB](/sequence-files/IGVFFI9302KDEB/), [IGVFFI9275ZMNQ](/sequence-files/IGVFFI9275ZMNQ/), [IGVFFI2939VUID](/sequence-files/IGVFFI2939VUID/), [IGVFFI4712WWMO](/sequence-files/IGVFFI4712WWMO/), [IGVFFI6220CJJS](/sequence-files/IGVFFI6220CJJS/), [IGVFFI4151HPPC](/sequence-files/IGVFFI4151HPPC/), [IGVFFI0917YRJC](/sequence-files/IGVFFI0917YRJC/), [IGVFFI1321DUBS](/sequence-files/IGVFFI1321DUBS/), [IGVFFI5992XUCU](/sequence-files/IGVFFI5992XUCU/), [IGVFFI5429KGUP](/sequence-files/IGVFFI5429KGUP/), [IGVFFI3642IOQG](/sequence-files/IGVFFI3642IOQG/), [IGVFFI6182DUUK](/sequence-files/IGVFFI6182DUUK/), [IGVFFI2167SQMA](/sequence-files/IGVFFI2167SQMA/), [IGVFFI6897VGAO](/sequence-files/IGVFFI6897VGAO/), [IGVFFI0296RHNQ](/sequence-files/IGVFFI0296RHNQ/), [IGVFFI3092RSYJ](/sequence-files/IGVFFI3092RSYJ/), [IGVFFI3359MYGY](/sequence-files/IGVFFI3359MYGY/), [IGVFFI4429FTBT](/sequence-files/IGVFFI4429FTBT/), [IGVFFI6932JMTL](/sequence-files/IGVFFI6932JMTL/), [IGVFFI0832ELWX](/sequence-files/IGVFFI0832ELWX/), [IGVFFI8978FICD](/sequence-files/IGVFFI8978FICD/), [IGVFFI5604YDMA](/sequence-files/IGVFFI5604YDMA/), [IGVFFI9895VNQK](/sequence-files/IGVFFI9895VNQK/), [IGVFFI8209ZUHX](/sequence-files/IGVFFI8209ZUHX/), [IGVFFI5531NSKH](/sequence-files/IGVFFI5531NSKH/), [IGVFFI4594GEMX](/sequence-files/IGVFFI4594GEMX/), [IGVFFI1696NEGU](/sequence-files/IGVFFI1696NEGU/), [IGVFFI3578CLFN](/sequence-files/IGVFFI3578CLFN/), [IGVFFI3070RHFT](/sequence-files/IGVFFI3070RHFT/), [IGVFFI0286LFLQ](/sequence-files/IGVFFI0286LFLQ/), [IGVFFI0292BVKK](/sequence-files/IGVFFI0292BVKK/), [IGVFFI5186PSYN](/sequence-files/IGVFFI5186PSYN/), [IGVFFI6400DTKK](/sequence-files/IGVFFI6400DTKK/), [IGVFFI4858HNCG](/sequence-files/IGVFFI4858HNCG/), [IGVFFI8127GGZP](/sequence-files/IGVFFI8127GGZP/), [IGVFFI2400PGDF](/sequence-files/IGVFFI2400PGDF/), [IGVFFI5464FKHL](/sequence-files/IGVFFI5464FKHL/) 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/IGVFDS9665GYVE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6463YBYJ](/in-vitro-systems/IGVFSM6463YBYJ/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6463YBYJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6463YBYJ](/in-vitro-systems/IGVFSM6463YBYJ/) 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/IGVFSM6463YBYJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9665GYVE](/measurement-sets/IGVFDS9665GYVE/) 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/IGVFDS9665GYVE/"
}
]
},
"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/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:50.020971+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/IGVFFI0230OXLP/",
"accession": "IGVFFI0230OXLP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:23:14.784537+00:00",
"file_format": "fastq",
"file_size": 7373967,
"href": "/sequence-files/IGVFFI0230OXLP/@@download/IGVFFI0230OXLP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/762aa2f7-5cc0-4506-90d9-ea48b8c6e3ad/IGVFFI0230OXLP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep8_S176_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9575KRZR/",
"accession": "IGVFFI9575KRZR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep10_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:17:46.411154+00:00",
"file_format": "fastq",
"file_size": 5501354,
"href": "/sequence-files/IGVFFI9575KRZR/@@download/IGVFFI9575KRZR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/545e1082-8620-40c7-8829-ab5201f59f30/IGVFFI9575KRZR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep10_S178_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5023RDPK/",
"accession": "IGVFFI5023RDPK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:21:54.995826+00:00",
"file_format": "fastq",
"file_size": 5925171,
"href": "/sequence-files/IGVFFI5023RDPK/@@download/IGVFFI5023RDPK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/142b42f7-9ac7-483d-9aa1-a2b9d017bee7/IGVFFI5023RDPK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep6_S174_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5868MZNY/",
"accession": "IGVFFI5868MZNY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:20:35.984173+00:00",
"file_format": "fastq",
"file_size": 1882662,
"href": "/sequence-files/IGVFFI5868MZNY/@@download/IGVFFI5868MZNY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/617c898f-90ad-4891-a61b-46231be09b29/IGVFFI5868MZNY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep4_S172_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2937OMXA/",
"accession": "IGVFFI2937OMXA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:21:19.900779+00:00",
"file_format": "fastq",
"file_size": 6045037,
"href": "/sequence-files/IGVFFI2937OMXA/@@download/IGVFFI2937OMXA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/16bbd439-2423-4699-bbee-7dcf80c455b4/IGVFFI2937OMXA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep5_S173_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5900PBEK/",
"accession": "IGVFFI5900PBEK",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:18:51.241643+00:00",
"file_format": "fastq",
"file_size": 1728660,
"href": "/sequence-files/IGVFFI5900PBEK/@@download/IGVFFI5900PBEK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/724268c6-69f7-4b18-9d56-5a5ebd015c30/IGVFFI5900PBEK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep12_S180_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0503EQVR/",
"accession": "IGVFFI0503EQVR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep10_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:17:55.115498+00:00",
"file_format": "fastq",
"file_size": 6825521,
"href": "/sequence-files/IGVFFI0503EQVR/@@download/IGVFFI0503EQVR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/73e43430-6725-4cd0-9448-8af9378c12eb/IGVFFI0503EQVR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep10_S178_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3119HSES/",
"accession": "IGVFFI3119HSES",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep11_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:18:25.106689+00:00",
"file_format": "fastq",
"file_size": 5446775,
"href": "/sequence-files/IGVFFI3119HSES/@@download/IGVFFI3119HSES.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bf96f69a-f7c7-4f62-9b87-fbe72303fa38/IGVFFI3119HSES.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep11_S179_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5806CXVA/",
"accession": "IGVFFI5806CXVA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep11_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:18:12.634553+00:00",
"file_format": "fastq",
"file_size": 1722891,
"href": "/sequence-files/IGVFFI5806CXVA/@@download/IGVFFI5806CXVA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9b733392-acdc-4901-aec1-c008462f0bad/IGVFFI5806CXVA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep11_S179_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8088FUDW/",
"accession": "IGVFFI8088FUDW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:19:26.031402+00:00",
"file_format": "fastq",
"file_size": 1942588,
"href": "/sequence-files/IGVFFI8088FUDW/@@download/IGVFFI8088FUDW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/00749da2-cc57-4ead-ab3c-e1048159949d/IGVFFI8088FUDW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC-PCRrep2_S170_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5944KRHZ/",
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"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "bdc26c18-93a6-41ca-b77c-dd78763a8e0a"
}