{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2708HTXW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2708HTXW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA_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 [IGVFSM8646DYNI](/in-vitro-systems/IGVFSM8646DYNI/) 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/IGVFSM8646DYNI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8646DYNI](/in-vitro-systems/IGVFSM8646DYNI/) 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/IGVFSM8646DYNI/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2708HTXW](/measurement-sets/IGVFDS2708HTXW/) 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/IGVFDS2708HTXW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2708HTXW](/measurement-sets/IGVFDS2708HTXW/) has sequence file(s) [IGVFFI1229MEEA](/sequence-files/IGVFFI1229MEEA/), [IGVFFI9139SKNU](/sequence-files/IGVFFI9139SKNU/), [IGVFFI4974TAPY](/sequence-files/IGVFFI4974TAPY/), [IGVFFI9140DDRI](/sequence-files/IGVFFI9140DDRI/), [IGVFFI8381CFTB](/sequence-files/IGVFFI8381CFTB/), [IGVFFI3859FMIK](/sequence-files/IGVFFI3859FMIK/), [IGVFFI7173EUOZ](/sequence-files/IGVFFI7173EUOZ/), [IGVFFI4197ZIYF](/sequence-files/IGVFFI4197ZIYF/), [IGVFFI4469XSVM](/sequence-files/IGVFFI4469XSVM/), [IGVFFI6350BRHA](/sequence-files/IGVFFI6350BRHA/), [IGVFFI6094CBUA](/sequence-files/IGVFFI6094CBUA/), [IGVFFI9726SQFG](/sequence-files/IGVFFI9726SQFG/), [IGVFFI0327VZDN](/sequence-files/IGVFFI0327VZDN/), [IGVFFI3918NSAB](/sequence-files/IGVFFI3918NSAB/), [IGVFFI2522ZZGZ](/sequence-files/IGVFFI2522ZZGZ/), [IGVFFI0943QPRC](/sequence-files/IGVFFI0943QPRC/), [IGVFFI7702NESZ](/sequence-files/IGVFFI7702NESZ/), [IGVFFI8734SUDB](/sequence-files/IGVFFI8734SUDB/), [IGVFFI0805UTCV](/sequence-files/IGVFFI0805UTCV/), [IGVFFI9493PKXZ](/sequence-files/IGVFFI9493PKXZ/), [IGVFFI0178FLZC](/sequence-files/IGVFFI0178FLZC/), [IGVFFI5856FKXC](/sequence-files/IGVFFI5856FKXC/), [IGVFFI2369QLGT](/sequence-files/IGVFFI2369QLGT/), [IGVFFI5892UBRB](/sequence-files/IGVFFI5892UBRB/), [IGVFFI6551FBMJ](/sequence-files/IGVFFI6551FBMJ/), [IGVFFI9357HYYG](/sequence-files/IGVFFI9357HYYG/), [IGVFFI6664FKEZ](/sequence-files/IGVFFI6664FKEZ/), [IGVFFI3132GSET](/sequence-files/IGVFFI3132GSET/), [IGVFFI0110IBGN](/sequence-files/IGVFFI0110IBGN/), [IGVFFI4348YOVA](/sequence-files/IGVFFI4348YOVA/), [IGVFFI7346YTFK](/sequence-files/IGVFFI7346YTFK/), [IGVFFI6083RUFQ](/sequence-files/IGVFFI6083RUFQ/), [IGVFFI6515THLX](/sequence-files/IGVFFI6515THLX/), [IGVFFI8318HDEK](/sequence-files/IGVFFI8318HDEK/), [IGVFFI5665PYZU](/sequence-files/IGVFFI5665PYZU/), [IGVFFI2296VPVS](/sequence-files/IGVFFI2296VPVS/), [IGVFFI6580BZXY](/sequence-files/IGVFFI6580BZXY/), [IGVFFI6843HAJB](/sequence-files/IGVFFI6843HAJB/), [IGVFFI4666JPYV](/sequence-files/IGVFFI4666JPYV/), [IGVFFI7693ARCI](/sequence-files/IGVFFI7693ARCI/), [IGVFFI6067FVTF](/sequence-files/IGVFFI6067FVTF/), [IGVFFI9351WCDC](/sequence-files/IGVFFI9351WCDC/), [IGVFFI1071JIIN](/sequence-files/IGVFFI1071JIIN/), [IGVFFI4810XFLN](/sequence-files/IGVFFI4810XFLN/), [IGVFFI3681NZAE](/sequence-files/IGVFFI3681NZAE/), [IGVFFI3750RLHU](/sequence-files/IGVFFI3750RLHU/), [IGVFFI9589TCDE](/sequence-files/IGVFFI9589TCDE/), [IGVFFI3487EAVL](/sequence-files/IGVFFI3487EAVL/) 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/IGVFDS2708HTXW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2708HTXW](/measurement-sets/IGVFDS2708HTXW/) has sequence file(s): [IGVFFI1229MEEA](/sequence-files/IGVFFI1229MEEA/), [IGVFFI9139SKNU](/sequence-files/IGVFFI9139SKNU/), [IGVFFI4974TAPY](/sequence-files/IGVFFI4974TAPY/), [IGVFFI9140DDRI](/sequence-files/IGVFFI9140DDRI/), [IGVFFI8381CFTB](/sequence-files/IGVFFI8381CFTB/), [IGVFFI3859FMIK](/sequence-files/IGVFFI3859FMIK/), [IGVFFI7173EUOZ](/sequence-files/IGVFFI7173EUOZ/), [IGVFFI4197ZIYF](/sequence-files/IGVFFI4197ZIYF/), [IGVFFI4469XSVM](/sequence-files/IGVFFI4469XSVM/), [IGVFFI6350BRHA](/sequence-files/IGVFFI6350BRHA/), [IGVFFI6094CBUA](/sequence-files/IGVFFI6094CBUA/), [IGVFFI9726SQFG](/sequence-files/IGVFFI9726SQFG/), [IGVFFI0327VZDN](/sequence-files/IGVFFI0327VZDN/), [IGVFFI3918NSAB](/sequence-files/IGVFFI3918NSAB/), [IGVFFI2522ZZGZ](/sequence-files/IGVFFI2522ZZGZ/), [IGVFFI0943QPRC](/sequence-files/IGVFFI0943QPRC/), [IGVFFI7702NESZ](/sequence-files/IGVFFI7702NESZ/), [IGVFFI8734SUDB](/sequence-files/IGVFFI8734SUDB/), [IGVFFI0805UTCV](/sequence-files/IGVFFI0805UTCV/), [IGVFFI9493PKXZ](/sequence-files/IGVFFI9493PKXZ/), [IGVFFI0178FLZC](/sequence-files/IGVFFI0178FLZC/), [IGVFFI5856FKXC](/sequence-files/IGVFFI5856FKXC/), [IGVFFI2369QLGT](/sequence-files/IGVFFI2369QLGT/), [IGVFFI5892UBRB](/sequence-files/IGVFFI5892UBRB/), [IGVFFI6551FBMJ](/sequence-files/IGVFFI6551FBMJ/), [IGVFFI9357HYYG](/sequence-files/IGVFFI9357HYYG/), [IGVFFI6664FKEZ](/sequence-files/IGVFFI6664FKEZ/), [IGVFFI3132GSET](/sequence-files/IGVFFI3132GSET/), [IGVFFI0110IBGN](/sequence-files/IGVFFI0110IBGN/), [IGVFFI4348YOVA](/sequence-files/IGVFFI4348YOVA/), [IGVFFI7346YTFK](/sequence-files/IGVFFI7346YTFK/), [IGVFFI6083RUFQ](/sequence-files/IGVFFI6083RUFQ/), [IGVFFI6515THLX](/sequence-files/IGVFFI6515THLX/), [IGVFFI8318HDEK](/sequence-files/IGVFFI8318HDEK/), [IGVFFI5665PYZU](/sequence-files/IGVFFI5665PYZU/), [IGVFFI2296VPVS](/sequence-files/IGVFFI2296VPVS/), [IGVFFI6580BZXY](/sequence-files/IGVFFI6580BZXY/), [IGVFFI6843HAJB](/sequence-files/IGVFFI6843HAJB/), [IGVFFI4666JPYV](/sequence-files/IGVFFI4666JPYV/), [IGVFFI7693ARCI](/sequence-files/IGVFFI7693ARCI/), [IGVFFI6067FVTF](/sequence-files/IGVFFI6067FVTF/), [IGVFFI9351WCDC](/sequence-files/IGVFFI9351WCDC/), [IGVFFI1071JIIN](/sequence-files/IGVFFI1071JIIN/), [IGVFFI4810XFLN](/sequence-files/IGVFFI4810XFLN/), [IGVFFI3681NZAE](/sequence-files/IGVFFI3681NZAE/), [IGVFFI3750RLHU](/sequence-files/IGVFFI3750RLHU/), [IGVFFI9589TCDE](/sequence-files/IGVFFI9589TCDE/), [IGVFFI3487EAVL](/sequence-files/IGVFFI3487EAVL/) 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/IGVFDS2708HTXW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2708HTXW](/measurement-sets/IGVFDS2708HTXW/) 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/IGVFDS2708HTXW/"
}
]
},
"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": "2023-12-01T00:04:41.209969+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/IGVFFI1229MEEA/",
"accession": "IGVFFI1229MEEA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:19.461000+00:00",
"file_format": "fastq",
"file_size": 3718873,
"href": "/sequence-files/IGVFFI1229MEEA/@@download/IGVFFI1229MEEA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3062288a-547d-4dac-b1b5-8ee4ad91a936/IGVFFI1229MEEA.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-BinA-PCRrep2_S2_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9139SKNU/",
"accession": "IGVFFI9139SKNU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:43.246855+00:00",
"file_format": "fastq",
"file_size": 4432624,
"href": "/sequence-files/IGVFFI9139SKNU/@@download/IGVFFI9139SKNU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2050ca22-a9c3-4152-9408-2515f4871a10/IGVFFI9139SKNU.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-BinA-PCRrep4_S4_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4974TAPY/",
"accession": "IGVFFI4974TAPY",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:32.672574+00:00",
"file_format": "fastq",
"file_size": 1472713,
"href": "/sequence-files/IGVFFI4974TAPY/@@download/IGVFFI4974TAPY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6318eb16-84be-4d03-b272-209e75d6f421/IGVFFI4974TAPY.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-BinA-PCRrep12_S102_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9140DDRI/",
"accession": "IGVFFI9140DDRI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep12_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:51.604638+00:00",
"file_format": "fastq",
"file_size": 7080302,
"href": "/sequence-files/IGVFFI9140DDRI/@@download/IGVFFI9140DDRI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3504816c-f308-4295-8c2f-2dc830e603b8/IGVFFI9140DDRI.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-BinA-PCRrep12_S102_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8381CFTB/",
"accession": "IGVFFI8381CFTB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:00.911007+00:00",
"file_format": "fastq",
"file_size": 918081,
"href": "/sequence-files/IGVFFI8381CFTB/@@download/IGVFFI8381CFTB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a73d0eef-5c64-47c0-aeb7-593565d4ffcd/IGVFFI8381CFTB.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-BinA-PCRrep2_S2_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3859FMIK/",
"accession": "IGVFFI3859FMIK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:24.686287+00:00",
"file_format": "fastq",
"file_size": 5916812,
"href": "/sequence-files/IGVFFI3859FMIK/@@download/IGVFFI3859FMIK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a3f45917-1684-488f-97a5-07514728a1fa/IGVFFI3859FMIK.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-BinA-PCRrep7_S97_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7173EUOZ/",
"accession": "IGVFFI7173EUOZ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep12_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:19.601713+00:00",
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"file_size": 1570467,
"href": "/sequence-files/IGVFFI7173EUOZ/@@download/IGVFFI7173EUOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7ef961d6-765c-4a47-90b1-7e3f52955433/IGVFFI7173EUOZ.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-FFrep1-BinA-PCRrep12_S102_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4197ZIYF/",
"accession": "IGVFFI4197ZIYF",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:06.018842+00:00",
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"file_size": 1626186,
"href": "/sequence-files/IGVFFI4197ZIYF/@@download/IGVFFI4197ZIYF.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4469XSVM/",
"accession": "IGVFFI4469XSVM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:01.855589+00:00",
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"file_size": 5497186,
"href": "/sequence-files/IGVFFI4469XSVM/@@download/IGVFFI4469XSVM.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-BinA-PCRrep8_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6350BRHA/",
"accession": "IGVFFI6350BRHA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:10.158428+00:00",
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"file_size": 926345,
"href": "/sequence-files/IGVFFI6350BRHA/@@download/IGVFFI6350BRHA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/69f8399e-56a4-4c8f-92e7-eeec256ab0fb/IGVFFI6350BRHA.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-BinA-PCRrep2_S2_I2_001.fastq.gz",
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"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:09:11.234578+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": "eaf2c3f2-0680-4c53-a3b2-5974796b9258"
}