{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2074JWFW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2074JWFW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-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 [IGVFDS2074JWFW](/measurement-sets/IGVFDS2074JWFW/) 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/IGVFDS2074JWFW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2074JWFW](/measurement-sets/IGVFDS2074JWFW/) has sequence file(s) [IGVFFI4502VLNC](/sequence-files/IGVFFI4502VLNC/), [IGVFFI0018KKLV](/sequence-files/IGVFFI0018KKLV/), [IGVFFI0005GBXS](/sequence-files/IGVFFI0005GBXS/), [IGVFFI8961TOUE](/sequence-files/IGVFFI8961TOUE/), [IGVFFI9937TZRF](/sequence-files/IGVFFI9937TZRF/), [IGVFFI3437ZCBU](/sequence-files/IGVFFI3437ZCBU/), [IGVFFI1306LCJK](/sequence-files/IGVFFI1306LCJK/), [IGVFFI4493GILB](/sequence-files/IGVFFI4493GILB/), [IGVFFI4792BZCN](/sequence-files/IGVFFI4792BZCN/), [IGVFFI1663XANF](/sequence-files/IGVFFI1663XANF/), [IGVFFI8634LQPV](/sequence-files/IGVFFI8634LQPV/), [IGVFFI6323EFQR](/sequence-files/IGVFFI6323EFQR/), [IGVFFI2826GLZC](/sequence-files/IGVFFI2826GLZC/), [IGVFFI1512CDIC](/sequence-files/IGVFFI1512CDIC/), [IGVFFI9470PXRU](/sequence-files/IGVFFI9470PXRU/), [IGVFFI3789NRLM](/sequence-files/IGVFFI3789NRLM/), [IGVFFI2848IXCA](/sequence-files/IGVFFI2848IXCA/), [IGVFFI1171KOAI](/sequence-files/IGVFFI1171KOAI/), [IGVFFI2110CXWO](/sequence-files/IGVFFI2110CXWO/), [IGVFFI3171WHRX](/sequence-files/IGVFFI3171WHRX/), [IGVFFI6386AKLI](/sequence-files/IGVFFI6386AKLI/), [IGVFFI4052CIEZ](/sequence-files/IGVFFI4052CIEZ/), [IGVFFI1524XVVI](/sequence-files/IGVFFI1524XVVI/), [IGVFFI3671LTUT](/sequence-files/IGVFFI3671LTUT/), [IGVFFI7724FMWK](/sequence-files/IGVFFI7724FMWK/), [IGVFFI1238BOFW](/sequence-files/IGVFFI1238BOFW/), [IGVFFI3455YCKJ](/sequence-files/IGVFFI3455YCKJ/), [IGVFFI6421BXBI](/sequence-files/IGVFFI6421BXBI/), [IGVFFI3571FKNU](/sequence-files/IGVFFI3571FKNU/), [IGVFFI4527QMXS](/sequence-files/IGVFFI4527QMXS/), [IGVFFI1688TLKS](/sequence-files/IGVFFI1688TLKS/), [IGVFFI3626XNDL](/sequence-files/IGVFFI3626XNDL/), [IGVFFI2120LBCS](/sequence-files/IGVFFI2120LBCS/), [IGVFFI6641EGJO](/sequence-files/IGVFFI6641EGJO/), [IGVFFI6390KMKF](/sequence-files/IGVFFI6390KMKF/), [IGVFFI7004TATT](/sequence-files/IGVFFI7004TATT/), [IGVFFI8365LVRA](/sequence-files/IGVFFI8365LVRA/), [IGVFFI1961ZHUD](/sequence-files/IGVFFI1961ZHUD/), [IGVFFI5535ICQI](/sequence-files/IGVFFI5535ICQI/), [IGVFFI2277SHRL](/sequence-files/IGVFFI2277SHRL/), [IGVFFI6756DAGQ](/sequence-files/IGVFFI6756DAGQ/), [IGVFFI5071HYKD](/sequence-files/IGVFFI5071HYKD/), [IGVFFI9278LVBS](/sequence-files/IGVFFI9278LVBS/), [IGVFFI5143RGFD](/sequence-files/IGVFFI5143RGFD/), [IGVFFI7162SGVY](/sequence-files/IGVFFI7162SGVY/), [IGVFFI5071NCAG](/sequence-files/IGVFFI5071NCAG/), [IGVFFI2650AOWQ](/sequence-files/IGVFFI2650AOWQ/), [IGVFFI5619NNEW](/sequence-files/IGVFFI5619NNEW/) 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/IGVFDS2074JWFW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2074JWFW](/measurement-sets/IGVFDS2074JWFW/) has sequence file(s): [IGVFFI4502VLNC](/sequence-files/IGVFFI4502VLNC/), [IGVFFI0018KKLV](/sequence-files/IGVFFI0018KKLV/), [IGVFFI0005GBXS](/sequence-files/IGVFFI0005GBXS/), [IGVFFI8961TOUE](/sequence-files/IGVFFI8961TOUE/), [IGVFFI9937TZRF](/sequence-files/IGVFFI9937TZRF/), [IGVFFI3437ZCBU](/sequence-files/IGVFFI3437ZCBU/), [IGVFFI1306LCJK](/sequence-files/IGVFFI1306LCJK/), [IGVFFI4493GILB](/sequence-files/IGVFFI4493GILB/), [IGVFFI4792BZCN](/sequence-files/IGVFFI4792BZCN/), [IGVFFI1663XANF](/sequence-files/IGVFFI1663XANF/), [IGVFFI8634LQPV](/sequence-files/IGVFFI8634LQPV/), [IGVFFI6323EFQR](/sequence-files/IGVFFI6323EFQR/), [IGVFFI2826GLZC](/sequence-files/IGVFFI2826GLZC/), [IGVFFI1512CDIC](/sequence-files/IGVFFI1512CDIC/), [IGVFFI9470PXRU](/sequence-files/IGVFFI9470PXRU/), [IGVFFI3789NRLM](/sequence-files/IGVFFI3789NRLM/), [IGVFFI2848IXCA](/sequence-files/IGVFFI2848IXCA/), [IGVFFI1171KOAI](/sequence-files/IGVFFI1171KOAI/), [IGVFFI2110CXWO](/sequence-files/IGVFFI2110CXWO/), [IGVFFI3171WHRX](/sequence-files/IGVFFI3171WHRX/), [IGVFFI6386AKLI](/sequence-files/IGVFFI6386AKLI/), [IGVFFI4052CIEZ](/sequence-files/IGVFFI4052CIEZ/), [IGVFFI1524XVVI](/sequence-files/IGVFFI1524XVVI/), [IGVFFI3671LTUT](/sequence-files/IGVFFI3671LTUT/), [IGVFFI7724FMWK](/sequence-files/IGVFFI7724FMWK/), [IGVFFI1238BOFW](/sequence-files/IGVFFI1238BOFW/), [IGVFFI3455YCKJ](/sequence-files/IGVFFI3455YCKJ/), [IGVFFI6421BXBI](/sequence-files/IGVFFI6421BXBI/), [IGVFFI3571FKNU](/sequence-files/IGVFFI3571FKNU/), [IGVFFI4527QMXS](/sequence-files/IGVFFI4527QMXS/), [IGVFFI1688TLKS](/sequence-files/IGVFFI1688TLKS/), [IGVFFI3626XNDL](/sequence-files/IGVFFI3626XNDL/), [IGVFFI2120LBCS](/sequence-files/IGVFFI2120LBCS/), [IGVFFI6641EGJO](/sequence-files/IGVFFI6641EGJO/), [IGVFFI6390KMKF](/sequence-files/IGVFFI6390KMKF/), [IGVFFI7004TATT](/sequence-files/IGVFFI7004TATT/), [IGVFFI8365LVRA](/sequence-files/IGVFFI8365LVRA/), [IGVFFI1961ZHUD](/sequence-files/IGVFFI1961ZHUD/), [IGVFFI5535ICQI](/sequence-files/IGVFFI5535ICQI/), [IGVFFI2277SHRL](/sequence-files/IGVFFI2277SHRL/), [IGVFFI6756DAGQ](/sequence-files/IGVFFI6756DAGQ/), [IGVFFI5071HYKD](/sequence-files/IGVFFI5071HYKD/), [IGVFFI9278LVBS](/sequence-files/IGVFFI9278LVBS/), [IGVFFI5143RGFD](/sequence-files/IGVFFI5143RGFD/), [IGVFFI7162SGVY](/sequence-files/IGVFFI7162SGVY/), [IGVFFI5071NCAG](/sequence-files/IGVFFI5071NCAG/), [IGVFFI2650AOWQ](/sequence-files/IGVFFI2650AOWQ/), [IGVFFI5619NNEW](/sequence-files/IGVFFI5619NNEW/) 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/IGVFDS2074JWFW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9725CVMG](/in-vitro-systems/IGVFSM9725CVMG/) 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/IGVFSM9725CVMG/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9725CVMG](/in-vitro-systems/IGVFSM9725CVMG/) 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/IGVFSM9725CVMG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2074JWFW](/measurement-sets/IGVFDS2074JWFW/) 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/IGVFDS2074JWFW/"
}
]
},
"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": "2023-11-30T22:49:16.680571+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/IGVFFI4502VLNC/",
"accession": "IGVFFI4502VLNC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:37:12.561708+00:00",
"file_format": "fastq",
"file_size": 871116,
"href": "/sequence-files/IGVFFI4502VLNC/@@download/IGVFFI4502VLNC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e7cd7812-2c8f-428f-add3-f23b3196890c/IGVFFI4502VLNC.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-FFrep2-BinC-PCRrep1_S265_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0018KKLV/",
"accession": "IGVFFI0018KKLV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:43:48.462337+00:00",
"file_format": "fastq",
"file_size": 3064760,
"href": "/sequence-files/IGVFFI0018KKLV/@@download/IGVFFI0018KKLV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/53c85db3-25e2-4cd9-986f-7c32233c097b/IGVFFI0018KKLV.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-FFrep2-BinC-PCRrep8_S362_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0005GBXS/",
"accession": "IGVFFI0005GBXS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:41:56.632396+00:00",
"file_format": "fastq",
"file_size": 3043310,
"href": "/sequence-files/IGVFFI0005GBXS/@@download/IGVFFI0005GBXS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7ad9caf9-328c-44ad-9c88-bcad10c05b17/IGVFFI0005GBXS.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-FFrep2-BinC-PCRrep5_S269_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8961TOUE/",
"accession": "IGVFFI8961TOUE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:42:15.312082+00:00",
"file_format": "fastq",
"file_size": 923346,
"href": "/sequence-files/IGVFFI8961TOUE/@@download/IGVFFI8961TOUE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dbb49ffb-c23e-4219-88c7-f40f6ebde119/IGVFFI8961TOUE.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-FFrep2-BinC-PCRrep6_S270_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9937TZRF/",
"accession": "IGVFFI9937TZRF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:43:39.325907+00:00",
"file_format": "fastq",
"file_size": 847886,
"href": "/sequence-files/IGVFFI9937TZRF/@@download/IGVFFI9937TZRF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/da27c17f-89c0-4b65-a8c3-ffc4133b5d78/IGVFFI9937TZRF.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-FFrep2-BinC-PCRrep8_S362_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3437ZCBU/",
"accession": "IGVFFI3437ZCBU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:41:08.403050+00:00",
"file_format": "fastq",
"file_size": 854491,
"href": "/sequence-files/IGVFFI3437ZCBU/@@download/IGVFFI3437ZCBU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/071ee7fd-67ff-48cb-adc6-7dd06726f10c/IGVFFI3437ZCBU.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-FFrep2-BinC-PCRrep4_S268_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1306LCJK/",
"accession": "IGVFFI1306LCJK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:39:53.243544+00:00",
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"href": "/sequence-files/IGVFFI1306LCJK/@@download/IGVFFI1306LCJK.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-FFrep2-BinC-PCRrep2_S266_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4493GILB/",
"accession": "IGVFFI4493GILB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:42:43.223177+00:00",
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"href": "/sequence-files/IGVFFI4493GILB/@@download/IGVFFI4493GILB.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4792BZCN/",
"accession": "IGVFFI4792BZCN",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:38:47.917679+00:00",
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"href": "/sequence-files/IGVFFI4792BZCN/@@download/IGVFFI4792BZCN.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-FFrep2-BinC-PCRrep11_S365_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1663XANF/",
"accession": "IGVFFI1663XANF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:40:30.780680+00:00",
"file_format": "fastq",
"file_size": 827275,
"href": "/sequence-files/IGVFFI1663XANF/@@download/IGVFFI1663XANF.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-FFrep2-BinC-PCRrep3_S267_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8634LQPV/",
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"submitted_files_timestamp": "2023-12-05T22:37:12.561708+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": "88718d19-7aa0-4ed7-8b52-8252474c0090"
}