{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1090HOMT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1090HOMT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-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 [IGVFDS1090HOMT](/measurement-sets/IGVFDS1090HOMT/) has sequence file(s) [IGVFFI1413JQBE](/sequence-files/IGVFFI1413JQBE/), [IGVFFI6051WFPM](/sequence-files/IGVFFI6051WFPM/), [IGVFFI2868KLGA](/sequence-files/IGVFFI2868KLGA/), [IGVFFI9131PRUC](/sequence-files/IGVFFI9131PRUC/), [IGVFFI4625MGCD](/sequence-files/IGVFFI4625MGCD/), [IGVFFI6745LMXY](/sequence-files/IGVFFI6745LMXY/), [IGVFFI9002MQHD](/sequence-files/IGVFFI9002MQHD/), [IGVFFI9742CAEY](/sequence-files/IGVFFI9742CAEY/), [IGVFFI5895BMUU](/sequence-files/IGVFFI5895BMUU/), [IGVFFI8305QMJX](/sequence-files/IGVFFI8305QMJX/), [IGVFFI8498QROT](/sequence-files/IGVFFI8498QROT/), [IGVFFI3358KRQQ](/sequence-files/IGVFFI3358KRQQ/), [IGVFFI9768XCHZ](/sequence-files/IGVFFI9768XCHZ/), [IGVFFI7677NZIN](/sequence-files/IGVFFI7677NZIN/), [IGVFFI5798SJLU](/sequence-files/IGVFFI5798SJLU/), [IGVFFI8164XVFS](/sequence-files/IGVFFI8164XVFS/), [IGVFFI4954NTMH](/sequence-files/IGVFFI4954NTMH/), [IGVFFI1671QBAR](/sequence-files/IGVFFI1671QBAR/), [IGVFFI9142XZPC](/sequence-files/IGVFFI9142XZPC/), [IGVFFI3921YTDC](/sequence-files/IGVFFI3921YTDC/), [IGVFFI1191AGWZ](/sequence-files/IGVFFI1191AGWZ/), [IGVFFI9983QKKH](/sequence-files/IGVFFI9983QKKH/), [IGVFFI2563XHZA](/sequence-files/IGVFFI2563XHZA/), [IGVFFI8513RZGF](/sequence-files/IGVFFI8513RZGF/), [IGVFFI4724UJBK](/sequence-files/IGVFFI4724UJBK/), [IGVFFI9641SBRA](/sequence-files/IGVFFI9641SBRA/), [IGVFFI6904UYIW](/sequence-files/IGVFFI6904UYIW/), [IGVFFI3937QEGY](/sequence-files/IGVFFI3937QEGY/), [IGVFFI1840UZRL](/sequence-files/IGVFFI1840UZRL/), [IGVFFI0174RPOJ](/sequence-files/IGVFFI0174RPOJ/), [IGVFFI1863EJWZ](/sequence-files/IGVFFI1863EJWZ/), [IGVFFI7714NLAF](/sequence-files/IGVFFI7714NLAF/), [IGVFFI6529YUYH](/sequence-files/IGVFFI6529YUYH/), [IGVFFI9571TTRD](/sequence-files/IGVFFI9571TTRD/), [IGVFFI3510YXIL](/sequence-files/IGVFFI3510YXIL/), [IGVFFI6831PUGB](/sequence-files/IGVFFI6831PUGB/), [IGVFFI6784VWKQ](/sequence-files/IGVFFI6784VWKQ/), [IGVFFI3527YRKS](/sequence-files/IGVFFI3527YRKS/), [IGVFFI0211JZQZ](/sequence-files/IGVFFI0211JZQZ/), [IGVFFI3063GMGR](/sequence-files/IGVFFI3063GMGR/), [IGVFFI5038IMRY](/sequence-files/IGVFFI5038IMRY/), [IGVFFI7624UAFP](/sequence-files/IGVFFI7624UAFP/), [IGVFFI5678YAKD](/sequence-files/IGVFFI5678YAKD/), [IGVFFI7372BGNV](/sequence-files/IGVFFI7372BGNV/), [IGVFFI0606VYNG](/sequence-files/IGVFFI0606VYNG/), [IGVFFI3049OLJB](/sequence-files/IGVFFI3049OLJB/), [IGVFFI2383HFQM](/sequence-files/IGVFFI2383HFQM/), [IGVFFI8716NTGM](/sequence-files/IGVFFI8716NTGM/) 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/IGVFDS1090HOMT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1090HOMT](/measurement-sets/IGVFDS1090HOMT/) has sequence file(s): [IGVFFI1413JQBE](/sequence-files/IGVFFI1413JQBE/), [IGVFFI6051WFPM](/sequence-files/IGVFFI6051WFPM/), [IGVFFI2868KLGA](/sequence-files/IGVFFI2868KLGA/), [IGVFFI9131PRUC](/sequence-files/IGVFFI9131PRUC/), [IGVFFI4625MGCD](/sequence-files/IGVFFI4625MGCD/), [IGVFFI6745LMXY](/sequence-files/IGVFFI6745LMXY/), [IGVFFI9002MQHD](/sequence-files/IGVFFI9002MQHD/), [IGVFFI9742CAEY](/sequence-files/IGVFFI9742CAEY/), [IGVFFI5895BMUU](/sequence-files/IGVFFI5895BMUU/), [IGVFFI8305QMJX](/sequence-files/IGVFFI8305QMJX/), [IGVFFI8498QROT](/sequence-files/IGVFFI8498QROT/), [IGVFFI3358KRQQ](/sequence-files/IGVFFI3358KRQQ/), [IGVFFI9768XCHZ](/sequence-files/IGVFFI9768XCHZ/), [IGVFFI7677NZIN](/sequence-files/IGVFFI7677NZIN/), [IGVFFI5798SJLU](/sequence-files/IGVFFI5798SJLU/), [IGVFFI8164XVFS](/sequence-files/IGVFFI8164XVFS/), [IGVFFI4954NTMH](/sequence-files/IGVFFI4954NTMH/), [IGVFFI1671QBAR](/sequence-files/IGVFFI1671QBAR/), [IGVFFI9142XZPC](/sequence-files/IGVFFI9142XZPC/), [IGVFFI3921YTDC](/sequence-files/IGVFFI3921YTDC/), [IGVFFI1191AGWZ](/sequence-files/IGVFFI1191AGWZ/), [IGVFFI9983QKKH](/sequence-files/IGVFFI9983QKKH/), [IGVFFI2563XHZA](/sequence-files/IGVFFI2563XHZA/), [IGVFFI8513RZGF](/sequence-files/IGVFFI8513RZGF/), [IGVFFI4724UJBK](/sequence-files/IGVFFI4724UJBK/), [IGVFFI9641SBRA](/sequence-files/IGVFFI9641SBRA/), [IGVFFI6904UYIW](/sequence-files/IGVFFI6904UYIW/), [IGVFFI3937QEGY](/sequence-files/IGVFFI3937QEGY/), [IGVFFI1840UZRL](/sequence-files/IGVFFI1840UZRL/), [IGVFFI0174RPOJ](/sequence-files/IGVFFI0174RPOJ/), [IGVFFI1863EJWZ](/sequence-files/IGVFFI1863EJWZ/), [IGVFFI7714NLAF](/sequence-files/IGVFFI7714NLAF/), [IGVFFI6529YUYH](/sequence-files/IGVFFI6529YUYH/), [IGVFFI9571TTRD](/sequence-files/IGVFFI9571TTRD/), [IGVFFI3510YXIL](/sequence-files/IGVFFI3510YXIL/), [IGVFFI6831PUGB](/sequence-files/IGVFFI6831PUGB/), [IGVFFI6784VWKQ](/sequence-files/IGVFFI6784VWKQ/), [IGVFFI3527YRKS](/sequence-files/IGVFFI3527YRKS/), [IGVFFI0211JZQZ](/sequence-files/IGVFFI0211JZQZ/), [IGVFFI3063GMGR](/sequence-files/IGVFFI3063GMGR/), [IGVFFI5038IMRY](/sequence-files/IGVFFI5038IMRY/), [IGVFFI7624UAFP](/sequence-files/IGVFFI7624UAFP/), [IGVFFI5678YAKD](/sequence-files/IGVFFI5678YAKD/), [IGVFFI7372BGNV](/sequence-files/IGVFFI7372BGNV/), [IGVFFI0606VYNG](/sequence-files/IGVFFI0606VYNG/), [IGVFFI3049OLJB](/sequence-files/IGVFFI3049OLJB/), [IGVFFI2383HFQM](/sequence-files/IGVFFI2383HFQM/), [IGVFFI8716NTGM](/sequence-files/IGVFFI8716NTGM/) 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/IGVFDS1090HOMT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1090HOMT](/measurement-sets/IGVFDS1090HOMT/) 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/IGVFDS1090HOMT/"
}
]
},
"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": "2024-11-25T23:54:37.075589+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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},
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},
{
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},
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},
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"@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": "2024-11-26T07:57:04.906474+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": "85586979-ad30-463c-9e16-6a322d7cf1c7"
}