{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7527SHUS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7527SHUS",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-BinB_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 [IGVFDS7527SHUS](/measurement-sets/IGVFDS7527SHUS/) has sequence file(s) [IGVFFI4517KTWA](/sequence-files/IGVFFI4517KTWA/), [IGVFFI6760QCEN](/sequence-files/IGVFFI6760QCEN/), [IGVFFI3614XBOM](/sequence-files/IGVFFI3614XBOM/), [IGVFFI3473AWGK](/sequence-files/IGVFFI3473AWGK/), [IGVFFI7621RHFQ](/sequence-files/IGVFFI7621RHFQ/), [IGVFFI8182FLAX](/sequence-files/IGVFFI8182FLAX/), [IGVFFI4871FYVA](/sequence-files/IGVFFI4871FYVA/), [IGVFFI6580AYKH](/sequence-files/IGVFFI6580AYKH/), [IGVFFI0944CKPS](/sequence-files/IGVFFI0944CKPS/), [IGVFFI1923HMKH](/sequence-files/IGVFFI1923HMKH/), [IGVFFI7919EUXI](/sequence-files/IGVFFI7919EUXI/), [IGVFFI7533XFWZ](/sequence-files/IGVFFI7533XFWZ/), [IGVFFI8545NHXP](/sequence-files/IGVFFI8545NHXP/), [IGVFFI1723XARB](/sequence-files/IGVFFI1723XARB/), [IGVFFI7217SAEN](/sequence-files/IGVFFI7217SAEN/), [IGVFFI0156XKVI](/sequence-files/IGVFFI0156XKVI/), [IGVFFI2518EUEN](/sequence-files/IGVFFI2518EUEN/), [IGVFFI4503TIMZ](/sequence-files/IGVFFI4503TIMZ/), [IGVFFI5847HPQQ](/sequence-files/IGVFFI5847HPQQ/), [IGVFFI0905BBDK](/sequence-files/IGVFFI0905BBDK/), [IGVFFI2918MWUC](/sequence-files/IGVFFI2918MWUC/), [IGVFFI2326EDTB](/sequence-files/IGVFFI2326EDTB/), [IGVFFI4843ODKR](/sequence-files/IGVFFI4843ODKR/), [IGVFFI0469ASPN](/sequence-files/IGVFFI0469ASPN/), [IGVFFI3748ZWWB](/sequence-files/IGVFFI3748ZWWB/), [IGVFFI4427CIVO](/sequence-files/IGVFFI4427CIVO/), [IGVFFI7799MFXT](/sequence-files/IGVFFI7799MFXT/), [IGVFFI6250CJLX](/sequence-files/IGVFFI6250CJLX/), [IGVFFI7445BTEW](/sequence-files/IGVFFI7445BTEW/), [IGVFFI9761VAKT](/sequence-files/IGVFFI9761VAKT/), [IGVFFI2032PQEY](/sequence-files/IGVFFI2032PQEY/), [IGVFFI8772MBNT](/sequence-files/IGVFFI8772MBNT/), [IGVFFI4699ENYN](/sequence-files/IGVFFI4699ENYN/), [IGVFFI6192ZNXU](/sequence-files/IGVFFI6192ZNXU/), [IGVFFI0928MWHT](/sequence-files/IGVFFI0928MWHT/), [IGVFFI8612JTHD](/sequence-files/IGVFFI8612JTHD/), [IGVFFI0184WVLY](/sequence-files/IGVFFI0184WVLY/), [IGVFFI4654DUIX](/sequence-files/IGVFFI4654DUIX/), [IGVFFI8990GDSE](/sequence-files/IGVFFI8990GDSE/), [IGVFFI2979ZOCL](/sequence-files/IGVFFI2979ZOCL/), [IGVFFI9609JGJD](/sequence-files/IGVFFI9609JGJD/), [IGVFFI8998JVUA](/sequence-files/IGVFFI8998JVUA/), [IGVFFI3807LPBP](/sequence-files/IGVFFI3807LPBP/), [IGVFFI7056WWJZ](/sequence-files/IGVFFI7056WWJZ/), [IGVFFI6048DDTW](/sequence-files/IGVFFI6048DDTW/), [IGVFFI2401NODT](/sequence-files/IGVFFI2401NODT/), [IGVFFI4998OPVG](/sequence-files/IGVFFI4998OPVG/), [IGVFFI0346GSPL](/sequence-files/IGVFFI0346GSPL/) 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/IGVFDS7527SHUS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7527SHUS](/measurement-sets/IGVFDS7527SHUS/) has sequence file(s): [IGVFFI4517KTWA](/sequence-files/IGVFFI4517KTWA/), [IGVFFI6760QCEN](/sequence-files/IGVFFI6760QCEN/), [IGVFFI3614XBOM](/sequence-files/IGVFFI3614XBOM/), [IGVFFI3473AWGK](/sequence-files/IGVFFI3473AWGK/), [IGVFFI7621RHFQ](/sequence-files/IGVFFI7621RHFQ/), [IGVFFI8182FLAX](/sequence-files/IGVFFI8182FLAX/), [IGVFFI4871FYVA](/sequence-files/IGVFFI4871FYVA/), [IGVFFI6580AYKH](/sequence-files/IGVFFI6580AYKH/), [IGVFFI0944CKPS](/sequence-files/IGVFFI0944CKPS/), [IGVFFI1923HMKH](/sequence-files/IGVFFI1923HMKH/), [IGVFFI7919EUXI](/sequence-files/IGVFFI7919EUXI/), [IGVFFI7533XFWZ](/sequence-files/IGVFFI7533XFWZ/), [IGVFFI8545NHXP](/sequence-files/IGVFFI8545NHXP/), [IGVFFI1723XARB](/sequence-files/IGVFFI1723XARB/), [IGVFFI7217SAEN](/sequence-files/IGVFFI7217SAEN/), [IGVFFI0156XKVI](/sequence-files/IGVFFI0156XKVI/), [IGVFFI2518EUEN](/sequence-files/IGVFFI2518EUEN/), [IGVFFI4503TIMZ](/sequence-files/IGVFFI4503TIMZ/), [IGVFFI5847HPQQ](/sequence-files/IGVFFI5847HPQQ/), [IGVFFI0905BBDK](/sequence-files/IGVFFI0905BBDK/), [IGVFFI2918MWUC](/sequence-files/IGVFFI2918MWUC/), [IGVFFI2326EDTB](/sequence-files/IGVFFI2326EDTB/), [IGVFFI4843ODKR](/sequence-files/IGVFFI4843ODKR/), [IGVFFI0469ASPN](/sequence-files/IGVFFI0469ASPN/), [IGVFFI3748ZWWB](/sequence-files/IGVFFI3748ZWWB/), [IGVFFI4427CIVO](/sequence-files/IGVFFI4427CIVO/), [IGVFFI7799MFXT](/sequence-files/IGVFFI7799MFXT/), [IGVFFI6250CJLX](/sequence-files/IGVFFI6250CJLX/), [IGVFFI7445BTEW](/sequence-files/IGVFFI7445BTEW/), [IGVFFI9761VAKT](/sequence-files/IGVFFI9761VAKT/), [IGVFFI2032PQEY](/sequence-files/IGVFFI2032PQEY/), [IGVFFI8772MBNT](/sequence-files/IGVFFI8772MBNT/), [IGVFFI4699ENYN](/sequence-files/IGVFFI4699ENYN/), [IGVFFI6192ZNXU](/sequence-files/IGVFFI6192ZNXU/), [IGVFFI0928MWHT](/sequence-files/IGVFFI0928MWHT/), [IGVFFI8612JTHD](/sequence-files/IGVFFI8612JTHD/), [IGVFFI0184WVLY](/sequence-files/IGVFFI0184WVLY/), [IGVFFI4654DUIX](/sequence-files/IGVFFI4654DUIX/), [IGVFFI8990GDSE](/sequence-files/IGVFFI8990GDSE/), [IGVFFI2979ZOCL](/sequence-files/IGVFFI2979ZOCL/), [IGVFFI9609JGJD](/sequence-files/IGVFFI9609JGJD/), [IGVFFI8998JVUA](/sequence-files/IGVFFI8998JVUA/), [IGVFFI3807LPBP](/sequence-files/IGVFFI3807LPBP/), [IGVFFI7056WWJZ](/sequence-files/IGVFFI7056WWJZ/), [IGVFFI6048DDTW](/sequence-files/IGVFFI6048DDTW/), [IGVFFI2401NODT](/sequence-files/IGVFFI2401NODT/), [IGVFFI4998OPVG](/sequence-files/IGVFFI4998OPVG/), [IGVFFI0346GSPL](/sequence-files/IGVFFI0346GSPL/) 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/IGVFDS7527SHUS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7527SHUS](/measurement-sets/IGVFDS7527SHUS/) 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/IGVFDS7527SHUS/"
}
]
},
"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": "2024-11-25T23:52:29.877016+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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"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 26-50% 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": "2024-11-26T06:25:31.387074+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": "74107772-d5ae-4341-8c5c-d720618fff4f"
}