{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9719TLJG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9719TLJG",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinD_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 [IGVFDS9719TLJG](/measurement-sets/IGVFDS9719TLJG/) has sequence file(s) [IGVFFI6515CXFG](/sequence-files/IGVFFI6515CXFG/), [IGVFFI3469ROBJ](/sequence-files/IGVFFI3469ROBJ/), [IGVFFI8967OETR](/sequence-files/IGVFFI8967OETR/), [IGVFFI5398AFVH](/sequence-files/IGVFFI5398AFVH/), [IGVFFI2878WPQO](/sequence-files/IGVFFI2878WPQO/), [IGVFFI1780VLLT](/sequence-files/IGVFFI1780VLLT/), [IGVFFI1071UCGG](/sequence-files/IGVFFI1071UCGG/), [IGVFFI2385AGWX](/sequence-files/IGVFFI2385AGWX/), [IGVFFI7900NWVW](/sequence-files/IGVFFI7900NWVW/), [IGVFFI3115KPXY](/sequence-files/IGVFFI3115KPXY/), [IGVFFI0382VPVJ](/sequence-files/IGVFFI0382VPVJ/), [IGVFFI6922DFYU](/sequence-files/IGVFFI6922DFYU/), [IGVFFI7308VLWN](/sequence-files/IGVFFI7308VLWN/), [IGVFFI0964THJW](/sequence-files/IGVFFI0964THJW/), [IGVFFI6075BHMZ](/sequence-files/IGVFFI6075BHMZ/), [IGVFFI3799NCCX](/sequence-files/IGVFFI3799NCCX/), [IGVFFI6663FKOJ](/sequence-files/IGVFFI6663FKOJ/), [IGVFFI8997KYJZ](/sequence-files/IGVFFI8997KYJZ/), [IGVFFI5218EJHS](/sequence-files/IGVFFI5218EJHS/), [IGVFFI2530KYTX](/sequence-files/IGVFFI2530KYTX/), [IGVFFI7261AWDM](/sequence-files/IGVFFI7261AWDM/), [IGVFFI5931ZGLQ](/sequence-files/IGVFFI5931ZGLQ/), [IGVFFI7261IAWJ](/sequence-files/IGVFFI7261IAWJ/), [IGVFFI8275GHLE](/sequence-files/IGVFFI8275GHLE/), [IGVFFI2065UBFV](/sequence-files/IGVFFI2065UBFV/), [IGVFFI4268ETMY](/sequence-files/IGVFFI4268ETMY/), [IGVFFI0239JATF](/sequence-files/IGVFFI0239JATF/), [IGVFFI3799QOHU](/sequence-files/IGVFFI3799QOHU/), [IGVFFI1366CYMV](/sequence-files/IGVFFI1366CYMV/), [IGVFFI7492UEXV](/sequence-files/IGVFFI7492UEXV/), [IGVFFI6587XSFM](/sequence-files/IGVFFI6587XSFM/), [IGVFFI5325KJIB](/sequence-files/IGVFFI5325KJIB/), [IGVFFI6940SYHQ](/sequence-files/IGVFFI6940SYHQ/), [IGVFFI5765ASKS](/sequence-files/IGVFFI5765ASKS/), [IGVFFI7511CYIV](/sequence-files/IGVFFI7511CYIV/), [IGVFFI8840JZVO](/sequence-files/IGVFFI8840JZVO/), [IGVFFI6026PRJQ](/sequence-files/IGVFFI6026PRJQ/), [IGVFFI2491OWOW](/sequence-files/IGVFFI2491OWOW/), [IGVFFI3746CBBD](/sequence-files/IGVFFI3746CBBD/), [IGVFFI0732SWOQ](/sequence-files/IGVFFI0732SWOQ/), [IGVFFI1285WULZ](/sequence-files/IGVFFI1285WULZ/), [IGVFFI6778GBHQ](/sequence-files/IGVFFI6778GBHQ/), [IGVFFI1603QEIE](/sequence-files/IGVFFI1603QEIE/), [IGVFFI6124KGOA](/sequence-files/IGVFFI6124KGOA/), [IGVFFI7122VMXB](/sequence-files/IGVFFI7122VMXB/), [IGVFFI7933EUWX](/sequence-files/IGVFFI7933EUWX/), [IGVFFI9386OVBT](/sequence-files/IGVFFI9386OVBT/), [IGVFFI7798XLLQ](/sequence-files/IGVFFI7798XLLQ/) 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/IGVFDS9719TLJG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9719TLJG](/measurement-sets/IGVFDS9719TLJG/) has sequence file(s): [IGVFFI6515CXFG](/sequence-files/IGVFFI6515CXFG/), [IGVFFI3469ROBJ](/sequence-files/IGVFFI3469ROBJ/), [IGVFFI8967OETR](/sequence-files/IGVFFI8967OETR/), [IGVFFI5398AFVH](/sequence-files/IGVFFI5398AFVH/), [IGVFFI2878WPQO](/sequence-files/IGVFFI2878WPQO/), [IGVFFI1780VLLT](/sequence-files/IGVFFI1780VLLT/), [IGVFFI1071UCGG](/sequence-files/IGVFFI1071UCGG/), [IGVFFI2385AGWX](/sequence-files/IGVFFI2385AGWX/), [IGVFFI7900NWVW](/sequence-files/IGVFFI7900NWVW/), [IGVFFI3115KPXY](/sequence-files/IGVFFI3115KPXY/), [IGVFFI0382VPVJ](/sequence-files/IGVFFI0382VPVJ/), [IGVFFI6922DFYU](/sequence-files/IGVFFI6922DFYU/), [IGVFFI7308VLWN](/sequence-files/IGVFFI7308VLWN/), [IGVFFI0964THJW](/sequence-files/IGVFFI0964THJW/), [IGVFFI6075BHMZ](/sequence-files/IGVFFI6075BHMZ/), [IGVFFI3799NCCX](/sequence-files/IGVFFI3799NCCX/), [IGVFFI6663FKOJ](/sequence-files/IGVFFI6663FKOJ/), [IGVFFI8997KYJZ](/sequence-files/IGVFFI8997KYJZ/), [IGVFFI5218EJHS](/sequence-files/IGVFFI5218EJHS/), [IGVFFI2530KYTX](/sequence-files/IGVFFI2530KYTX/), [IGVFFI7261AWDM](/sequence-files/IGVFFI7261AWDM/), [IGVFFI5931ZGLQ](/sequence-files/IGVFFI5931ZGLQ/), [IGVFFI7261IAWJ](/sequence-files/IGVFFI7261IAWJ/), [IGVFFI8275GHLE](/sequence-files/IGVFFI8275GHLE/), [IGVFFI2065UBFV](/sequence-files/IGVFFI2065UBFV/), [IGVFFI4268ETMY](/sequence-files/IGVFFI4268ETMY/), [IGVFFI0239JATF](/sequence-files/IGVFFI0239JATF/), [IGVFFI3799QOHU](/sequence-files/IGVFFI3799QOHU/), [IGVFFI1366CYMV](/sequence-files/IGVFFI1366CYMV/), [IGVFFI7492UEXV](/sequence-files/IGVFFI7492UEXV/), [IGVFFI6587XSFM](/sequence-files/IGVFFI6587XSFM/), [IGVFFI5325KJIB](/sequence-files/IGVFFI5325KJIB/), [IGVFFI6940SYHQ](/sequence-files/IGVFFI6940SYHQ/), [IGVFFI5765ASKS](/sequence-files/IGVFFI5765ASKS/), [IGVFFI7511CYIV](/sequence-files/IGVFFI7511CYIV/), [IGVFFI8840JZVO](/sequence-files/IGVFFI8840JZVO/), [IGVFFI6026PRJQ](/sequence-files/IGVFFI6026PRJQ/), [IGVFFI2491OWOW](/sequence-files/IGVFFI2491OWOW/), [IGVFFI3746CBBD](/sequence-files/IGVFFI3746CBBD/), [IGVFFI0732SWOQ](/sequence-files/IGVFFI0732SWOQ/), [IGVFFI1285WULZ](/sequence-files/IGVFFI1285WULZ/), [IGVFFI6778GBHQ](/sequence-files/IGVFFI6778GBHQ/), [IGVFFI1603QEIE](/sequence-files/IGVFFI1603QEIE/), [IGVFFI6124KGOA](/sequence-files/IGVFFI6124KGOA/), [IGVFFI7122VMXB](/sequence-files/IGVFFI7122VMXB/), [IGVFFI7933EUWX](/sequence-files/IGVFFI7933EUWX/), [IGVFFI9386OVBT](/sequence-files/IGVFFI9386OVBT/), [IGVFFI7798XLLQ](/sequence-files/IGVFFI7798XLLQ/) 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/IGVFDS9719TLJG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9719TLJG](/measurement-sets/IGVFDS9719TLJG/) 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/IGVFDS9719TLJG/"
}
]
},
"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"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:52:37.491305+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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"accession": "IGVFFI6515CXFG",
"aliases": [
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"upload_status": "validated"
},
{
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},
{
"@id": "/sequence-files/IGVFFI8967OETR/",
"accession": "IGVFFI8967OETR",
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},
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},
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},
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},
{
"@id": "/sequence-files/IGVFFI1071UCGG/",
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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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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0382VPVJ/",
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],
"content_type": "reads",
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"creation_timestamp": "2024-11-26T06:26:05.240252+00:00",
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"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 76-100% 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": "2024-11-26T06:26:05.240252+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": "529ee181-f410-4fd9-8da1-8fcde57aed39"
}