{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4670KYYZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4670KYYZ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinB_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 [IGVFSM1664NEGX](/in-vitro-systems/IGVFSM1664NEGX/) 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/IGVFSM1664NEGX/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4670KYYZ](/measurement-sets/IGVFDS4670KYYZ/) has in progress subobject auxiliary set [IGVFDS9749LVSS](/auxiliary-sets/IGVFDS9749LVSS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4670KYYZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4670KYYZ](/measurement-sets/IGVFDS4670KYYZ/) 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/IGVFDS4670KYYZ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9749LVSS](/auxiliary-sets/IGVFDS9749LVSS/) has sequence file(s): [IGVFFI7687UKFE](/sequence-files/IGVFFI7687UKFE/), [IGVFFI9028MKBY](/sequence-files/IGVFFI9028MKBY/), [IGVFFI6090LUFD](/sequence-files/IGVFFI6090LUFD/), [IGVFFI2324NATU](/sequence-files/IGVFFI2324NATU/), [IGVFFI9562EIRT](/sequence-files/IGVFFI9562EIRT/), [IGVFFI1103JKJA](/sequence-files/IGVFFI1103JKJA/), [IGVFFI5870OEWI](/sequence-files/IGVFFI5870OEWI/), [IGVFFI2241UJGM](/sequence-files/IGVFFI2241UJGM/), [IGVFFI7390SQZF](/sequence-files/IGVFFI7390SQZF/), [IGVFFI1656FMUD](/sequence-files/IGVFFI1656FMUD/), [IGVFFI6213HMWS](/sequence-files/IGVFFI6213HMWS/), [IGVFFI7935LZEB](/sequence-files/IGVFFI7935LZEB/), [IGVFFI0491YOPG](/sequence-files/IGVFFI0491YOPG/), [IGVFFI0188PLMA](/sequence-files/IGVFFI0188PLMA/), [IGVFFI0573DKSX](/sequence-files/IGVFFI0573DKSX/), [IGVFFI3697ELZW](/sequence-files/IGVFFI3697ELZW/), [IGVFFI5480ZZJF](/sequence-files/IGVFFI5480ZZJF/), [IGVFFI7548XQCE](/sequence-files/IGVFFI7548XQCE/), [IGVFFI6138BEDC](/sequence-files/IGVFFI6138BEDC/), [IGVFFI4935LPFU](/sequence-files/IGVFFI4935LPFU/), [IGVFFI9735KPOY](/sequence-files/IGVFFI9735KPOY/), [IGVFFI9241EJHI](/sequence-files/IGVFFI9241EJHI/), [IGVFFI1267WKCI](/sequence-files/IGVFFI1267WKCI/), [IGVFFI2450MTRN](/sequence-files/IGVFFI2450MTRN/), [IGVFFI6473WCCA](/sequence-files/IGVFFI6473WCCA/), [IGVFFI2481LCHM](/sequence-files/IGVFFI2481LCHM/), [IGVFFI8426TADQ](/sequence-files/IGVFFI8426TADQ/), [IGVFFI5515WMAP](/sequence-files/IGVFFI5515WMAP/), [IGVFFI4889NNJC](/sequence-files/IGVFFI4889NNJC/), [IGVFFI4755OYJJ](/sequence-files/IGVFFI4755OYJJ/), [IGVFFI6265FFWL](/sequence-files/IGVFFI6265FFWL/), [IGVFFI2596LZGM](/sequence-files/IGVFFI2596LZGM/), [IGVFFI3981PZOM](/sequence-files/IGVFFI3981PZOM/), [IGVFFI0891GHBS](/sequence-files/IGVFFI0891GHBS/), [IGVFFI5825CPPI](/sequence-files/IGVFFI5825CPPI/), [IGVFFI6831GAHM](/sequence-files/IGVFFI6831GAHM/), [IGVFFI8417PWAV](/sequence-files/IGVFFI8417PWAV/), [IGVFFI7475HSYH](/sequence-files/IGVFFI7475HSYH/), [IGVFFI8765NOHD](/sequence-files/IGVFFI8765NOHD/), [IGVFFI3701VQZK](/sequence-files/IGVFFI3701VQZK/), [IGVFFI9229UGYP](/sequence-files/IGVFFI9229UGYP/), [IGVFFI9998LGTM](/sequence-files/IGVFFI9998LGTM/), [IGVFFI9171MTAP](/sequence-files/IGVFFI9171MTAP/), [IGVFFI1930WYDB](/sequence-files/IGVFFI1930WYDB/), [IGVFFI7419GTGG](/sequence-files/IGVFFI7419GTGG/), [IGVFFI1618NTXS](/sequence-files/IGVFFI1618NTXS/), [IGVFFI8545WBNH](/sequence-files/IGVFFI8545WBNH/), [IGVFFI0557PYCK](/sequence-files/IGVFFI0557PYCK/) 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/IGVFDS9749LVSS/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9749LVSS](/auxiliary-sets/IGVFDS9749LVSS/) has sequence file(s) [IGVFFI7687UKFE](/sequence-files/IGVFFI7687UKFE/), [IGVFFI9028MKBY](/sequence-files/IGVFFI9028MKBY/), [IGVFFI6090LUFD](/sequence-files/IGVFFI6090LUFD/), [IGVFFI2324NATU](/sequence-files/IGVFFI2324NATU/), [IGVFFI9562EIRT](/sequence-files/IGVFFI9562EIRT/), [IGVFFI1103JKJA](/sequence-files/IGVFFI1103JKJA/), [IGVFFI5870OEWI](/sequence-files/IGVFFI5870OEWI/), [IGVFFI2241UJGM](/sequence-files/IGVFFI2241UJGM/), [IGVFFI7390SQZF](/sequence-files/IGVFFI7390SQZF/), [IGVFFI1656FMUD](/sequence-files/IGVFFI1656FMUD/), [IGVFFI6213HMWS](/sequence-files/IGVFFI6213HMWS/), [IGVFFI7935LZEB](/sequence-files/IGVFFI7935LZEB/), [IGVFFI0491YOPG](/sequence-files/IGVFFI0491YOPG/), [IGVFFI0188PLMA](/sequence-files/IGVFFI0188PLMA/), [IGVFFI0573DKSX](/sequence-files/IGVFFI0573DKSX/), [IGVFFI3697ELZW](/sequence-files/IGVFFI3697ELZW/), [IGVFFI5480ZZJF](/sequence-files/IGVFFI5480ZZJF/), [IGVFFI7548XQCE](/sequence-files/IGVFFI7548XQCE/), [IGVFFI6138BEDC](/sequence-files/IGVFFI6138BEDC/), [IGVFFI4935LPFU](/sequence-files/IGVFFI4935LPFU/), [IGVFFI9735KPOY](/sequence-files/IGVFFI9735KPOY/), [IGVFFI9241EJHI](/sequence-files/IGVFFI9241EJHI/), [IGVFFI1267WKCI](/sequence-files/IGVFFI1267WKCI/), [IGVFFI2450MTRN](/sequence-files/IGVFFI2450MTRN/), [IGVFFI6473WCCA](/sequence-files/IGVFFI6473WCCA/), [IGVFFI2481LCHM](/sequence-files/IGVFFI2481LCHM/), [IGVFFI8426TADQ](/sequence-files/IGVFFI8426TADQ/), [IGVFFI5515WMAP](/sequence-files/IGVFFI5515WMAP/), [IGVFFI4889NNJC](/sequence-files/IGVFFI4889NNJC/), [IGVFFI4755OYJJ](/sequence-files/IGVFFI4755OYJJ/), [IGVFFI6265FFWL](/sequence-files/IGVFFI6265FFWL/), [IGVFFI2596LZGM](/sequence-files/IGVFFI2596LZGM/), [IGVFFI3981PZOM](/sequence-files/IGVFFI3981PZOM/), [IGVFFI0891GHBS](/sequence-files/IGVFFI0891GHBS/), [IGVFFI5825CPPI](/sequence-files/IGVFFI5825CPPI/), [IGVFFI6831GAHM](/sequence-files/IGVFFI6831GAHM/), [IGVFFI8417PWAV](/sequence-files/IGVFFI8417PWAV/), [IGVFFI7475HSYH](/sequence-files/IGVFFI7475HSYH/), [IGVFFI8765NOHD](/sequence-files/IGVFFI8765NOHD/), [IGVFFI3701VQZK](/sequence-files/IGVFFI3701VQZK/), [IGVFFI9229UGYP](/sequence-files/IGVFFI9229UGYP/), [IGVFFI9998LGTM](/sequence-files/IGVFFI9998LGTM/), [IGVFFI9171MTAP](/sequence-files/IGVFFI9171MTAP/), [IGVFFI1930WYDB](/sequence-files/IGVFFI1930WYDB/), [IGVFFI7419GTGG](/sequence-files/IGVFFI7419GTGG/), [IGVFFI1618NTXS](/sequence-files/IGVFFI1618NTXS/), [IGVFFI8545WBNH](/sequence-files/IGVFFI8545WBNH/), [IGVFFI0557PYCK](/sequence-files/IGVFFI0557PYCK/) 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/IGVFDS9749LVSS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9749LVSS](/auxiliary-sets/IGVFDS9749LVSS/) 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/IGVFDS9749LVSS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9749LVSS/",
"accession": "IGVFDS9749LVSS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinB_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": "2023-11-30T22:49:26.775500+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": "2023-12-20T23:05:53.289257+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1664NEGX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1664NEGX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinB"
],
"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 26-50% 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": "2023-12-05T23:31:52.730380+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": "2b400e92-5e5d-4f84-8476-a368204bbc60"
}