{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0987HUNS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0987HUNS",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinA_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 [IGVFDS0987HUNS](/measurement-sets/IGVFDS0987HUNS/) has sequence file(s) [IGVFFI7981YZEQ](/sequence-files/IGVFFI7981YZEQ/), [IGVFFI4111NFKC](/sequence-files/IGVFFI4111NFKC/), [IGVFFI4175AMDN](/sequence-files/IGVFFI4175AMDN/), [IGVFFI3046ZFNT](/sequence-files/IGVFFI3046ZFNT/), [IGVFFI2114BNAD](/sequence-files/IGVFFI2114BNAD/), [IGVFFI2782LCYJ](/sequence-files/IGVFFI2782LCYJ/), [IGVFFI6910BTOW](/sequence-files/IGVFFI6910BTOW/), [IGVFFI1532MJDB](/sequence-files/IGVFFI1532MJDB/), [IGVFFI0744IKLC](/sequence-files/IGVFFI0744IKLC/), [IGVFFI5538LBFQ](/sequence-files/IGVFFI5538LBFQ/), [IGVFFI9369UTLT](/sequence-files/IGVFFI9369UTLT/), [IGVFFI3446ZYAD](/sequence-files/IGVFFI3446ZYAD/), [IGVFFI2511HOYF](/sequence-files/IGVFFI2511HOYF/), [IGVFFI2815UOCB](/sequence-files/IGVFFI2815UOCB/), [IGVFFI0765YQQA](/sequence-files/IGVFFI0765YQQA/), [IGVFFI7442IWAT](/sequence-files/IGVFFI7442IWAT/), [IGVFFI2230EJVA](/sequence-files/IGVFFI2230EJVA/), [IGVFFI1398ROPC](/sequence-files/IGVFFI1398ROPC/), [IGVFFI8026LRYM](/sequence-files/IGVFFI8026LRYM/), [IGVFFI3860VWWK](/sequence-files/IGVFFI3860VWWK/), [IGVFFI9469MKTM](/sequence-files/IGVFFI9469MKTM/), [IGVFFI9638FWCB](/sequence-files/IGVFFI9638FWCB/), [IGVFFI6225YDNP](/sequence-files/IGVFFI6225YDNP/), [IGVFFI6086LLYF](/sequence-files/IGVFFI6086LLYF/), [IGVFFI7211YTLW](/sequence-files/IGVFFI7211YTLW/), [IGVFFI3695CCVM](/sequence-files/IGVFFI3695CCVM/), [IGVFFI0654PIMT](/sequence-files/IGVFFI0654PIMT/), [IGVFFI2322ECNQ](/sequence-files/IGVFFI2322ECNQ/), [IGVFFI7082YTHR](/sequence-files/IGVFFI7082YTHR/), [IGVFFI0689QEXH](/sequence-files/IGVFFI0689QEXH/), [IGVFFI3935AQHJ](/sequence-files/IGVFFI3935AQHJ/), [IGVFFI4064ZITQ](/sequence-files/IGVFFI4064ZITQ/), [IGVFFI2884UHUV](/sequence-files/IGVFFI2884UHUV/), [IGVFFI4065RLRO](/sequence-files/IGVFFI4065RLRO/), [IGVFFI3795CZNX](/sequence-files/IGVFFI3795CZNX/), [IGVFFI3585BVZS](/sequence-files/IGVFFI3585BVZS/), [IGVFFI8439JZFO](/sequence-files/IGVFFI8439JZFO/), [IGVFFI7902VCZA](/sequence-files/IGVFFI7902VCZA/), [IGVFFI4517SLFD](/sequence-files/IGVFFI4517SLFD/), [IGVFFI9247KADL](/sequence-files/IGVFFI9247KADL/), [IGVFFI8931MDQQ](/sequence-files/IGVFFI8931MDQQ/), [IGVFFI1465UTEB](/sequence-files/IGVFFI1465UTEB/), [IGVFFI3378CQHK](/sequence-files/IGVFFI3378CQHK/), [IGVFFI8947WGPU](/sequence-files/IGVFFI8947WGPU/), [IGVFFI2797TYNM](/sequence-files/IGVFFI2797TYNM/), [IGVFFI5447HFXR](/sequence-files/IGVFFI5447HFXR/), [IGVFFI2083SOOR](/sequence-files/IGVFFI2083SOOR/), [IGVFFI4038TZXB](/sequence-files/IGVFFI4038TZXB/) 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/IGVFDS0987HUNS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0987HUNS](/measurement-sets/IGVFDS0987HUNS/) has sequence file(s): [IGVFFI7981YZEQ](/sequence-files/IGVFFI7981YZEQ/), [IGVFFI4111NFKC](/sequence-files/IGVFFI4111NFKC/), [IGVFFI4175AMDN](/sequence-files/IGVFFI4175AMDN/), [IGVFFI3046ZFNT](/sequence-files/IGVFFI3046ZFNT/), [IGVFFI2114BNAD](/sequence-files/IGVFFI2114BNAD/), [IGVFFI2782LCYJ](/sequence-files/IGVFFI2782LCYJ/), [IGVFFI6910BTOW](/sequence-files/IGVFFI6910BTOW/), [IGVFFI1532MJDB](/sequence-files/IGVFFI1532MJDB/), [IGVFFI0744IKLC](/sequence-files/IGVFFI0744IKLC/), [IGVFFI5538LBFQ](/sequence-files/IGVFFI5538LBFQ/), [IGVFFI9369UTLT](/sequence-files/IGVFFI9369UTLT/), [IGVFFI3446ZYAD](/sequence-files/IGVFFI3446ZYAD/), [IGVFFI2511HOYF](/sequence-files/IGVFFI2511HOYF/), [IGVFFI2815UOCB](/sequence-files/IGVFFI2815UOCB/), [IGVFFI0765YQQA](/sequence-files/IGVFFI0765YQQA/), [IGVFFI7442IWAT](/sequence-files/IGVFFI7442IWAT/), [IGVFFI2230EJVA](/sequence-files/IGVFFI2230EJVA/), [IGVFFI1398ROPC](/sequence-files/IGVFFI1398ROPC/), [IGVFFI8026LRYM](/sequence-files/IGVFFI8026LRYM/), [IGVFFI3860VWWK](/sequence-files/IGVFFI3860VWWK/), [IGVFFI9469MKTM](/sequence-files/IGVFFI9469MKTM/), [IGVFFI9638FWCB](/sequence-files/IGVFFI9638FWCB/), [IGVFFI6225YDNP](/sequence-files/IGVFFI6225YDNP/), [IGVFFI6086LLYF](/sequence-files/IGVFFI6086LLYF/), [IGVFFI7211YTLW](/sequence-files/IGVFFI7211YTLW/), [IGVFFI3695CCVM](/sequence-files/IGVFFI3695CCVM/), [IGVFFI0654PIMT](/sequence-files/IGVFFI0654PIMT/), [IGVFFI2322ECNQ](/sequence-files/IGVFFI2322ECNQ/), [IGVFFI7082YTHR](/sequence-files/IGVFFI7082YTHR/), [IGVFFI0689QEXH](/sequence-files/IGVFFI0689QEXH/), [IGVFFI3935AQHJ](/sequence-files/IGVFFI3935AQHJ/), [IGVFFI4064ZITQ](/sequence-files/IGVFFI4064ZITQ/), [IGVFFI2884UHUV](/sequence-files/IGVFFI2884UHUV/), [IGVFFI4065RLRO](/sequence-files/IGVFFI4065RLRO/), [IGVFFI3795CZNX](/sequence-files/IGVFFI3795CZNX/), [IGVFFI3585BVZS](/sequence-files/IGVFFI3585BVZS/), [IGVFFI8439JZFO](/sequence-files/IGVFFI8439JZFO/), [IGVFFI7902VCZA](/sequence-files/IGVFFI7902VCZA/), [IGVFFI4517SLFD](/sequence-files/IGVFFI4517SLFD/), [IGVFFI9247KADL](/sequence-files/IGVFFI9247KADL/), [IGVFFI8931MDQQ](/sequence-files/IGVFFI8931MDQQ/), [IGVFFI1465UTEB](/sequence-files/IGVFFI1465UTEB/), [IGVFFI3378CQHK](/sequence-files/IGVFFI3378CQHK/), [IGVFFI8947WGPU](/sequence-files/IGVFFI8947WGPU/), [IGVFFI2797TYNM](/sequence-files/IGVFFI2797TYNM/), [IGVFFI5447HFXR](/sequence-files/IGVFFI5447HFXR/), [IGVFFI2083SOOR](/sequence-files/IGVFFI2083SOOR/), [IGVFFI4038TZXB](/sequence-files/IGVFFI4038TZXB/) 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/IGVFDS0987HUNS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0987HUNS](/measurement-sets/IGVFDS0987HUNS/) 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/IGVFDS0987HUNS/"
}
]
},
"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": [
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],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:46.950043+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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"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 0-25% 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": "2024-11-26T07:25:22.493245+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": "1c22790f-b230-4455-ba46-ecb1bca492cd"
}