{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9571BWRT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9571BWRT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5553HMSC](/in-vitro-systems/IGVFSM5553HMSC/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5553HMSC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9571BWRT](/measurement-sets/IGVFDS9571BWRT/) has in progress subobject auxiliary set [IGVFDS0206NGEM](/auxiliary-sets/IGVFDS0206NGEM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9571BWRT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0206NGEM](/auxiliary-sets/IGVFDS0206NGEM/) has sequence file(s): [IGVFFI9303YWBP](/sequence-files/IGVFFI9303YWBP/), [IGVFFI8646MCTV](/sequence-files/IGVFFI8646MCTV/), [IGVFFI7942HNDY](/sequence-files/IGVFFI7942HNDY/), [IGVFFI3064COLS](/sequence-files/IGVFFI3064COLS/), [IGVFFI8587DIVE](/sequence-files/IGVFFI8587DIVE/), [IGVFFI7837AIQF](/sequence-files/IGVFFI7837AIQF/), [IGVFFI9163PWKU](/sequence-files/IGVFFI9163PWKU/), [IGVFFI1831CQZA](/sequence-files/IGVFFI1831CQZA/), [IGVFFI7712IPYT](/sequence-files/IGVFFI7712IPYT/), [IGVFFI7809FCWW](/sequence-files/IGVFFI7809FCWW/), [IGVFFI1473RHJI](/sequence-files/IGVFFI1473RHJI/), [IGVFFI8100NFAY](/sequence-files/IGVFFI8100NFAY/), [IGVFFI0806LQXD](/sequence-files/IGVFFI0806LQXD/), [IGVFFI7918SIPE](/sequence-files/IGVFFI7918SIPE/), [IGVFFI6059CQXT](/sequence-files/IGVFFI6059CQXT/), [IGVFFI1697QMTO](/sequence-files/IGVFFI1697QMTO/), [IGVFFI9674YRFE](/sequence-files/IGVFFI9674YRFE/), [IGVFFI8927QBZK](/sequence-files/IGVFFI8927QBZK/), [IGVFFI0778JHDP](/sequence-files/IGVFFI0778JHDP/), [IGVFFI3637QTSQ](/sequence-files/IGVFFI3637QTSQ/), [IGVFFI9438FFWV](/sequence-files/IGVFFI9438FFWV/), [IGVFFI4897RYLH](/sequence-files/IGVFFI4897RYLH/), [IGVFFI5344GIHZ](/sequence-files/IGVFFI5344GIHZ/), [IGVFFI3683RKVR](/sequence-files/IGVFFI3683RKVR/), [IGVFFI7771FUKK](/sequence-files/IGVFFI7771FUKK/), [IGVFFI0802AXQK](/sequence-files/IGVFFI0802AXQK/), [IGVFFI6638XTWS](/sequence-files/IGVFFI6638XTWS/), [IGVFFI3574NFSF](/sequence-files/IGVFFI3574NFSF/), [IGVFFI7085FRRK](/sequence-files/IGVFFI7085FRRK/), [IGVFFI3223ICUH](/sequence-files/IGVFFI3223ICUH/), [IGVFFI5427BOAK](/sequence-files/IGVFFI5427BOAK/), [IGVFFI8723YIZI](/sequence-files/IGVFFI8723YIZI/), [IGVFFI6448IQOJ](/sequence-files/IGVFFI6448IQOJ/), [IGVFFI6932AHRJ](/sequence-files/IGVFFI6932AHRJ/), [IGVFFI9103QGHK](/sequence-files/IGVFFI9103QGHK/), [IGVFFI9529AFJP](/sequence-files/IGVFFI9529AFJP/), [IGVFFI2847IJWO](/sequence-files/IGVFFI2847IJWO/), [IGVFFI5774NHHM](/sequence-files/IGVFFI5774NHHM/), [IGVFFI2100YJBK](/sequence-files/IGVFFI2100YJBK/), [IGVFFI6271FAOS](/sequence-files/IGVFFI6271FAOS/), [IGVFFI0549SHDW](/sequence-files/IGVFFI0549SHDW/), [IGVFFI9094FEXS](/sequence-files/IGVFFI9094FEXS/), [IGVFFI6362VAKU](/sequence-files/IGVFFI6362VAKU/), [IGVFFI1565IYIK](/sequence-files/IGVFFI1565IYIK/), [IGVFFI3292EQHB](/sequence-files/IGVFFI3292EQHB/), [IGVFFI9012RFFO](/sequence-files/IGVFFI9012RFFO/), [IGVFFI0860PEYW](/sequence-files/IGVFFI0860PEYW/), [IGVFFI0366RVXY](/sequence-files/IGVFFI0366RVXY/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0206NGEM/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9571BWRT](/measurement-sets/IGVFDS9571BWRT/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS9571BWRT/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0206NGEM](/auxiliary-sets/IGVFDS0206NGEM/) has sequence file(s) [IGVFFI9303YWBP](/sequence-files/IGVFFI9303YWBP/), [IGVFFI8646MCTV](/sequence-files/IGVFFI8646MCTV/), [IGVFFI7942HNDY](/sequence-files/IGVFFI7942HNDY/), [IGVFFI3064COLS](/sequence-files/IGVFFI3064COLS/), [IGVFFI8587DIVE](/sequence-files/IGVFFI8587DIVE/), [IGVFFI7837AIQF](/sequence-files/IGVFFI7837AIQF/), [IGVFFI9163PWKU](/sequence-files/IGVFFI9163PWKU/), [IGVFFI1831CQZA](/sequence-files/IGVFFI1831CQZA/), [IGVFFI7712IPYT](/sequence-files/IGVFFI7712IPYT/), [IGVFFI7809FCWW](/sequence-files/IGVFFI7809FCWW/), [IGVFFI1473RHJI](/sequence-files/IGVFFI1473RHJI/), [IGVFFI8100NFAY](/sequence-files/IGVFFI8100NFAY/), [IGVFFI0806LQXD](/sequence-files/IGVFFI0806LQXD/), [IGVFFI7918SIPE](/sequence-files/IGVFFI7918SIPE/), [IGVFFI6059CQXT](/sequence-files/IGVFFI6059CQXT/), [IGVFFI1697QMTO](/sequence-files/IGVFFI1697QMTO/), [IGVFFI9674YRFE](/sequence-files/IGVFFI9674YRFE/), [IGVFFI8927QBZK](/sequence-files/IGVFFI8927QBZK/), [IGVFFI0778JHDP](/sequence-files/IGVFFI0778JHDP/), [IGVFFI3637QTSQ](/sequence-files/IGVFFI3637QTSQ/), [IGVFFI9438FFWV](/sequence-files/IGVFFI9438FFWV/), [IGVFFI4897RYLH](/sequence-files/IGVFFI4897RYLH/), [IGVFFI5344GIHZ](/sequence-files/IGVFFI5344GIHZ/), [IGVFFI3683RKVR](/sequence-files/IGVFFI3683RKVR/), [IGVFFI7771FUKK](/sequence-files/IGVFFI7771FUKK/), [IGVFFI0802AXQK](/sequence-files/IGVFFI0802AXQK/), [IGVFFI6638XTWS](/sequence-files/IGVFFI6638XTWS/), [IGVFFI3574NFSF](/sequence-files/IGVFFI3574NFSF/), [IGVFFI7085FRRK](/sequence-files/IGVFFI7085FRRK/), [IGVFFI3223ICUH](/sequence-files/IGVFFI3223ICUH/), [IGVFFI5427BOAK](/sequence-files/IGVFFI5427BOAK/), [IGVFFI8723YIZI](/sequence-files/IGVFFI8723YIZI/), [IGVFFI6448IQOJ](/sequence-files/IGVFFI6448IQOJ/), [IGVFFI6932AHRJ](/sequence-files/IGVFFI6932AHRJ/), [IGVFFI9103QGHK](/sequence-files/IGVFFI9103QGHK/), [IGVFFI9529AFJP](/sequence-files/IGVFFI9529AFJP/), [IGVFFI2847IJWO](/sequence-files/IGVFFI2847IJWO/), [IGVFFI5774NHHM](/sequence-files/IGVFFI5774NHHM/), [IGVFFI2100YJBK](/sequence-files/IGVFFI2100YJBK/), [IGVFFI6271FAOS](/sequence-files/IGVFFI6271FAOS/), [IGVFFI0549SHDW](/sequence-files/IGVFFI0549SHDW/), [IGVFFI9094FEXS](/sequence-files/IGVFFI9094FEXS/), [IGVFFI6362VAKU](/sequence-files/IGVFFI6362VAKU/), [IGVFFI1565IYIK](/sequence-files/IGVFFI1565IYIK/), [IGVFFI3292EQHB](/sequence-files/IGVFFI3292EQHB/), [IGVFFI9012RFFO](/sequence-files/IGVFFI9012RFFO/), [IGVFFI0860PEYW](/sequence-files/IGVFFI0860PEYW/), [IGVFFI0366RVXY](/sequence-files/IGVFFI0366RVXY/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0206NGEM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0206NGEM](/auxiliary-sets/IGVFDS0206NGEM/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS0206NGEM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0206NGEM/",
"accession": "IGVFDS0206NGEM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:04:44.582533+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:06:57.510049+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5553HMSC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5553HMSC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"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": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:25:40.244528+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"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": "0bc8eb39-dac6-4c4c-82d5-348f89325d97"
}