{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5295ONUY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5295ONUY",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5295ONUY](/measurement-sets/IGVFDS5295ONUY/) has sequence file(s) [IGVFFI8637GOMS](/sequence-files/IGVFFI8637GOMS/), [IGVFFI3686KHAB](/sequence-files/IGVFFI3686KHAB/), [IGVFFI0629VACY](/sequence-files/IGVFFI0629VACY/), [IGVFFI9754YQCF](/sequence-files/IGVFFI9754YQCF/), [IGVFFI1286DEIO](/sequence-files/IGVFFI1286DEIO/), [IGVFFI2374KTTR](/sequence-files/IGVFFI2374KTTR/), [IGVFFI5120VGVX](/sequence-files/IGVFFI5120VGVX/), [IGVFFI0516TIVA](/sequence-files/IGVFFI0516TIVA/), [IGVFFI5661QEDZ](/sequence-files/IGVFFI5661QEDZ/), [IGVFFI3930ENEX](/sequence-files/IGVFFI3930ENEX/), [IGVFFI4785CTVI](/sequence-files/IGVFFI4785CTVI/), [IGVFFI7993JOPX](/sequence-files/IGVFFI7993JOPX/), [IGVFFI6145YKNS](/sequence-files/IGVFFI6145YKNS/), [IGVFFI9855BQZR](/sequence-files/IGVFFI9855BQZR/), [IGVFFI4256CQHO](/sequence-files/IGVFFI4256CQHO/), [IGVFFI9143ZHIG](/sequence-files/IGVFFI9143ZHIG/), [IGVFFI6883VUKZ](/sequence-files/IGVFFI6883VUKZ/), [IGVFFI7697HJSI](/sequence-files/IGVFFI7697HJSI/), [IGVFFI9881EHIQ](/sequence-files/IGVFFI9881EHIQ/), [IGVFFI1935NEBQ](/sequence-files/IGVFFI1935NEBQ/), [IGVFFI6705CQOA](/sequence-files/IGVFFI6705CQOA/), [IGVFFI6462RCQU](/sequence-files/IGVFFI6462RCQU/), [IGVFFI8529ERDW](/sequence-files/IGVFFI8529ERDW/), [IGVFFI8560BRCT](/sequence-files/IGVFFI8560BRCT/), [IGVFFI0203GKFQ](/sequence-files/IGVFFI0203GKFQ/), [IGVFFI3152KQOV](/sequence-files/IGVFFI3152KQOV/), [IGVFFI4732QYAW](/sequence-files/IGVFFI4732QYAW/), [IGVFFI1282OERO](/sequence-files/IGVFFI1282OERO/), [IGVFFI6767UCBB](/sequence-files/IGVFFI6767UCBB/), [IGVFFI3239WBMC](/sequence-files/IGVFFI3239WBMC/), [IGVFFI2866MJXM](/sequence-files/IGVFFI2866MJXM/), [IGVFFI8540CZBA](/sequence-files/IGVFFI8540CZBA/), [IGVFFI2738WAUY](/sequence-files/IGVFFI2738WAUY/), [IGVFFI7311VVRJ](/sequence-files/IGVFFI7311VVRJ/), [IGVFFI1250OHCN](/sequence-files/IGVFFI1250OHCN/), [IGVFFI4264DRAA](/sequence-files/IGVFFI4264DRAA/), [IGVFFI0541QZJU](/sequence-files/IGVFFI0541QZJU/), [IGVFFI5755KEMF](/sequence-files/IGVFFI5755KEMF/), [IGVFFI5903OLBX](/sequence-files/IGVFFI5903OLBX/), [IGVFFI5846WLZC](/sequence-files/IGVFFI5846WLZC/), [IGVFFI5833BYKF](/sequence-files/IGVFFI5833BYKF/), [IGVFFI2515AACF](/sequence-files/IGVFFI2515AACF/), [IGVFFI4785YNZB](/sequence-files/IGVFFI4785YNZB/), [IGVFFI5758FIMB](/sequence-files/IGVFFI5758FIMB/), [IGVFFI4213ZCCE](/sequence-files/IGVFFI4213ZCCE/), [IGVFFI0575EIPJ](/sequence-files/IGVFFI0575EIPJ/), [IGVFFI9758RDOH](/sequence-files/IGVFFI9758RDOH/), [IGVFFI8431JXWO](/sequence-files/IGVFFI8431JXWO/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5295ONUY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5295ONUY](/measurement-sets/IGVFDS5295ONUY/) has sequence file(s): [IGVFFI8637GOMS](/sequence-files/IGVFFI8637GOMS/), [IGVFFI3686KHAB](/sequence-files/IGVFFI3686KHAB/), [IGVFFI0629VACY](/sequence-files/IGVFFI0629VACY/), [IGVFFI9754YQCF](/sequence-files/IGVFFI9754YQCF/), [IGVFFI1286DEIO](/sequence-files/IGVFFI1286DEIO/), [IGVFFI2374KTTR](/sequence-files/IGVFFI2374KTTR/), [IGVFFI5120VGVX](/sequence-files/IGVFFI5120VGVX/), [IGVFFI0516TIVA](/sequence-files/IGVFFI0516TIVA/), [IGVFFI5661QEDZ](/sequence-files/IGVFFI5661QEDZ/), [IGVFFI3930ENEX](/sequence-files/IGVFFI3930ENEX/), [IGVFFI4785CTVI](/sequence-files/IGVFFI4785CTVI/), [IGVFFI7993JOPX](/sequence-files/IGVFFI7993JOPX/), [IGVFFI6145YKNS](/sequence-files/IGVFFI6145YKNS/), [IGVFFI9855BQZR](/sequence-files/IGVFFI9855BQZR/), [IGVFFI4256CQHO](/sequence-files/IGVFFI4256CQHO/), [IGVFFI9143ZHIG](/sequence-files/IGVFFI9143ZHIG/), [IGVFFI6883VUKZ](/sequence-files/IGVFFI6883VUKZ/), [IGVFFI7697HJSI](/sequence-files/IGVFFI7697HJSI/), [IGVFFI9881EHIQ](/sequence-files/IGVFFI9881EHIQ/), [IGVFFI1935NEBQ](/sequence-files/IGVFFI1935NEBQ/), [IGVFFI6705CQOA](/sequence-files/IGVFFI6705CQOA/), [IGVFFI6462RCQU](/sequence-files/IGVFFI6462RCQU/), [IGVFFI8529ERDW](/sequence-files/IGVFFI8529ERDW/), [IGVFFI8560BRCT](/sequence-files/IGVFFI8560BRCT/), [IGVFFI0203GKFQ](/sequence-files/IGVFFI0203GKFQ/), [IGVFFI3152KQOV](/sequence-files/IGVFFI3152KQOV/), [IGVFFI4732QYAW](/sequence-files/IGVFFI4732QYAW/), [IGVFFI1282OERO](/sequence-files/IGVFFI1282OERO/), [IGVFFI6767UCBB](/sequence-files/IGVFFI6767UCBB/), [IGVFFI3239WBMC](/sequence-files/IGVFFI3239WBMC/), [IGVFFI2866MJXM](/sequence-files/IGVFFI2866MJXM/), [IGVFFI8540CZBA](/sequence-files/IGVFFI8540CZBA/), [IGVFFI2738WAUY](/sequence-files/IGVFFI2738WAUY/), [IGVFFI7311VVRJ](/sequence-files/IGVFFI7311VVRJ/), [IGVFFI1250OHCN](/sequence-files/IGVFFI1250OHCN/), [IGVFFI4264DRAA](/sequence-files/IGVFFI4264DRAA/), [IGVFFI0541QZJU](/sequence-files/IGVFFI0541QZJU/), [IGVFFI5755KEMF](/sequence-files/IGVFFI5755KEMF/), [IGVFFI5903OLBX](/sequence-files/IGVFFI5903OLBX/), [IGVFFI5846WLZC](/sequence-files/IGVFFI5846WLZC/), [IGVFFI5833BYKF](/sequence-files/IGVFFI5833BYKF/), [IGVFFI2515AACF](/sequence-files/IGVFFI2515AACF/), [IGVFFI4785YNZB](/sequence-files/IGVFFI4785YNZB/), [IGVFFI5758FIMB](/sequence-files/IGVFFI5758FIMB/), [IGVFFI4213ZCCE](/sequence-files/IGVFFI4213ZCCE/), [IGVFFI0575EIPJ](/sequence-files/IGVFFI0575EIPJ/), [IGVFFI9758RDOH](/sequence-files/IGVFFI9758RDOH/), [IGVFFI8431JXWO](/sequence-files/IGVFFI8431JXWO/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5295ONUY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5295ONUY](/measurement-sets/IGVFDS5295ONUY/) 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/IGVFDS5295ONUY/"
}
]
},
"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"
},
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{
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"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:52:34.215253+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",
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{
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"aliases": [
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},
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},
{
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},
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},
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},
{
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],
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"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T06:25:48.014956+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS 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": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "6994eb82-730c-4633-acf0-203a442edbd9"
}