{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5956AIUB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5956AIUB",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-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 [IGVFDS5956AIUB](/measurement-sets/IGVFDS5956AIUB/) has sequence file(s) [IGVFFI8845BFBO](/sequence-files/IGVFFI8845BFBO/), [IGVFFI7535FHYN](/sequence-files/IGVFFI7535FHYN/), [IGVFFI4086URHX](/sequence-files/IGVFFI4086URHX/), [IGVFFI6602ZOPG](/sequence-files/IGVFFI6602ZOPG/), [IGVFFI7053OTTC](/sequence-files/IGVFFI7053OTTC/), [IGVFFI7796CCCS](/sequence-files/IGVFFI7796CCCS/), [IGVFFI6177OKBG](/sequence-files/IGVFFI6177OKBG/), [IGVFFI0821UGBJ](/sequence-files/IGVFFI0821UGBJ/), [IGVFFI0022RTCR](/sequence-files/IGVFFI0022RTCR/), [IGVFFI4010KKPI](/sequence-files/IGVFFI4010KKPI/), [IGVFFI9500AIGT](/sequence-files/IGVFFI9500AIGT/), [IGVFFI0947PEAA](/sequence-files/IGVFFI0947PEAA/), [IGVFFI2085SFHP](/sequence-files/IGVFFI2085SFHP/), [IGVFFI6667HAWT](/sequence-files/IGVFFI6667HAWT/), [IGVFFI7743QXVJ](/sequence-files/IGVFFI7743QXVJ/), [IGVFFI7258QLSS](/sequence-files/IGVFFI7258QLSS/), [IGVFFI3897UWGW](/sequence-files/IGVFFI3897UWGW/), [IGVFFI3231GPCD](/sequence-files/IGVFFI3231GPCD/), [IGVFFI2594WNYR](/sequence-files/IGVFFI2594WNYR/), [IGVFFI4281UJOO](/sequence-files/IGVFFI4281UJOO/), [IGVFFI8138QELJ](/sequence-files/IGVFFI8138QELJ/), [IGVFFI8302UKGH](/sequence-files/IGVFFI8302UKGH/), [IGVFFI3872CIIK](/sequence-files/IGVFFI3872CIIK/), [IGVFFI6814THCR](/sequence-files/IGVFFI6814THCR/), [IGVFFI3185KTKB](/sequence-files/IGVFFI3185KTKB/), [IGVFFI9922PLKW](/sequence-files/IGVFFI9922PLKW/), [IGVFFI4175JNYL](/sequence-files/IGVFFI4175JNYL/), [IGVFFI3599AFGH](/sequence-files/IGVFFI3599AFGH/), [IGVFFI4332JVPR](/sequence-files/IGVFFI4332JVPR/), [IGVFFI1240LMNX](/sequence-files/IGVFFI1240LMNX/), [IGVFFI8782XEIK](/sequence-files/IGVFFI8782XEIK/), [IGVFFI5323WMCW](/sequence-files/IGVFFI5323WMCW/), [IGVFFI4631AGTV](/sequence-files/IGVFFI4631AGTV/), [IGVFFI9184CKPO](/sequence-files/IGVFFI9184CKPO/), [IGVFFI5822CJHD](/sequence-files/IGVFFI5822CJHD/), [IGVFFI4591ESRZ](/sequence-files/IGVFFI4591ESRZ/), [IGVFFI8219FPYL](/sequence-files/IGVFFI8219FPYL/), [IGVFFI6319OPLY](/sequence-files/IGVFFI6319OPLY/), [IGVFFI9227IAKG](/sequence-files/IGVFFI9227IAKG/), [IGVFFI3403MCHJ](/sequence-files/IGVFFI3403MCHJ/), [IGVFFI5601SAIA](/sequence-files/IGVFFI5601SAIA/), [IGVFFI9816QOYV](/sequence-files/IGVFFI9816QOYV/), [IGVFFI9790GOHG](/sequence-files/IGVFFI9790GOHG/), [IGVFFI8823CBRH](/sequence-files/IGVFFI8823CBRH/), [IGVFFI6830LTVM](/sequence-files/IGVFFI6830LTVM/), [IGVFFI8905NZAJ](/sequence-files/IGVFFI8905NZAJ/), [IGVFFI5088CLCD](/sequence-files/IGVFFI5088CLCD/), [IGVFFI6545OZAJ](/sequence-files/IGVFFI6545OZAJ/) 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/IGVFDS5956AIUB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5956AIUB](/measurement-sets/IGVFDS5956AIUB/) has sequence file(s): [IGVFFI8845BFBO](/sequence-files/IGVFFI8845BFBO/), [IGVFFI7535FHYN](/sequence-files/IGVFFI7535FHYN/), [IGVFFI4086URHX](/sequence-files/IGVFFI4086URHX/), [IGVFFI6602ZOPG](/sequence-files/IGVFFI6602ZOPG/), [IGVFFI7053OTTC](/sequence-files/IGVFFI7053OTTC/), [IGVFFI7796CCCS](/sequence-files/IGVFFI7796CCCS/), [IGVFFI6177OKBG](/sequence-files/IGVFFI6177OKBG/), [IGVFFI0821UGBJ](/sequence-files/IGVFFI0821UGBJ/), [IGVFFI0022RTCR](/sequence-files/IGVFFI0022RTCR/), [IGVFFI4010KKPI](/sequence-files/IGVFFI4010KKPI/), [IGVFFI9500AIGT](/sequence-files/IGVFFI9500AIGT/), [IGVFFI0947PEAA](/sequence-files/IGVFFI0947PEAA/), [IGVFFI2085SFHP](/sequence-files/IGVFFI2085SFHP/), [IGVFFI6667HAWT](/sequence-files/IGVFFI6667HAWT/), [IGVFFI7743QXVJ](/sequence-files/IGVFFI7743QXVJ/), [IGVFFI7258QLSS](/sequence-files/IGVFFI7258QLSS/), [IGVFFI3897UWGW](/sequence-files/IGVFFI3897UWGW/), [IGVFFI3231GPCD](/sequence-files/IGVFFI3231GPCD/), [IGVFFI2594WNYR](/sequence-files/IGVFFI2594WNYR/), [IGVFFI4281UJOO](/sequence-files/IGVFFI4281UJOO/), [IGVFFI8138QELJ](/sequence-files/IGVFFI8138QELJ/), [IGVFFI8302UKGH](/sequence-files/IGVFFI8302UKGH/), [IGVFFI3872CIIK](/sequence-files/IGVFFI3872CIIK/), [IGVFFI6814THCR](/sequence-files/IGVFFI6814THCR/), [IGVFFI3185KTKB](/sequence-files/IGVFFI3185KTKB/), [IGVFFI9922PLKW](/sequence-files/IGVFFI9922PLKW/), [IGVFFI4175JNYL](/sequence-files/IGVFFI4175JNYL/), [IGVFFI3599AFGH](/sequence-files/IGVFFI3599AFGH/), [IGVFFI4332JVPR](/sequence-files/IGVFFI4332JVPR/), [IGVFFI1240LMNX](/sequence-files/IGVFFI1240LMNX/), [IGVFFI8782XEIK](/sequence-files/IGVFFI8782XEIK/), [IGVFFI5323WMCW](/sequence-files/IGVFFI5323WMCW/), [IGVFFI4631AGTV](/sequence-files/IGVFFI4631AGTV/), [IGVFFI9184CKPO](/sequence-files/IGVFFI9184CKPO/), [IGVFFI5822CJHD](/sequence-files/IGVFFI5822CJHD/), [IGVFFI4591ESRZ](/sequence-files/IGVFFI4591ESRZ/), [IGVFFI8219FPYL](/sequence-files/IGVFFI8219FPYL/), [IGVFFI6319OPLY](/sequence-files/IGVFFI6319OPLY/), [IGVFFI9227IAKG](/sequence-files/IGVFFI9227IAKG/), [IGVFFI3403MCHJ](/sequence-files/IGVFFI3403MCHJ/), [IGVFFI5601SAIA](/sequence-files/IGVFFI5601SAIA/), [IGVFFI9816QOYV](/sequence-files/IGVFFI9816QOYV/), [IGVFFI9790GOHG](/sequence-files/IGVFFI9790GOHG/), [IGVFFI8823CBRH](/sequence-files/IGVFFI8823CBRH/), [IGVFFI6830LTVM](/sequence-files/IGVFFI6830LTVM/), [IGVFFI8905NZAJ](/sequence-files/IGVFFI8905NZAJ/), [IGVFFI5088CLCD](/sequence-files/IGVFFI5088CLCD/), [IGVFFI6545OZAJ](/sequence-files/IGVFFI6545OZAJ/) 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/IGVFDS5956AIUB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5956AIUB](/measurement-sets/IGVFDS5956AIUB/) 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/IGVFDS5956AIUB/"
}
]
},
"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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{
"@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": "2024-11-25T23:52:17.516464+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": "IGVFFI8845BFBO",
"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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],
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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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},
{
"@id": "/sequence-files/IGVFFI9500AIGT/",
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],
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"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 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": "2024-11-26T06:10:38.305537+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": "e8cd26b6-3747-41b7-beb3-65497070d0fd"
}