{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8339LZYX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8339LZYX",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-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 [IGVFSM9470HNZI](/in-vitro-systems/IGVFSM9470HNZI/) 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/IGVFSM9470HNZI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8339LZYX](/measurement-sets/IGVFDS8339LZYX/) has in progress subobject auxiliary set [IGVFDS7133IGCV](/auxiliary-sets/IGVFDS7133IGCV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8339LZYX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8339LZYX](/measurement-sets/IGVFDS8339LZYX/) 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/IGVFDS8339LZYX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7133IGCV](/auxiliary-sets/IGVFDS7133IGCV/) has sequence file(s): [IGVFFI1368LSCJ](/sequence-files/IGVFFI1368LSCJ/), [IGVFFI6696BZYA](/sequence-files/IGVFFI6696BZYA/), [IGVFFI9305KZOV](/sequence-files/IGVFFI9305KZOV/), [IGVFFI1085QHKS](/sequence-files/IGVFFI1085QHKS/), [IGVFFI4908VVVZ](/sequence-files/IGVFFI4908VVVZ/), [IGVFFI1621EULU](/sequence-files/IGVFFI1621EULU/), [IGVFFI4297AHZA](/sequence-files/IGVFFI4297AHZA/), [IGVFFI1446IIUH](/sequence-files/IGVFFI1446IIUH/), [IGVFFI1131DQUS](/sequence-files/IGVFFI1131DQUS/), [IGVFFI4165XEYG](/sequence-files/IGVFFI4165XEYG/), [IGVFFI9459ZYJC](/sequence-files/IGVFFI9459ZYJC/), [IGVFFI2891JOLR](/sequence-files/IGVFFI2891JOLR/), [IGVFFI7951MGOG](/sequence-files/IGVFFI7951MGOG/), [IGVFFI9417QZSJ](/sequence-files/IGVFFI9417QZSJ/), [IGVFFI2771VDEV](/sequence-files/IGVFFI2771VDEV/), [IGVFFI1672XROW](/sequence-files/IGVFFI1672XROW/), [IGVFFI5251WUBT](/sequence-files/IGVFFI5251WUBT/), [IGVFFI2393SXQP](/sequence-files/IGVFFI2393SXQP/), [IGVFFI2535BTAI](/sequence-files/IGVFFI2535BTAI/), [IGVFFI1696NTIX](/sequence-files/IGVFFI1696NTIX/), [IGVFFI0025YWDI](/sequence-files/IGVFFI0025YWDI/), [IGVFFI8725MRSD](/sequence-files/IGVFFI8725MRSD/), [IGVFFI2968SOPK](/sequence-files/IGVFFI2968SOPK/), [IGVFFI3021EADH](/sequence-files/IGVFFI3021EADH/), [IGVFFI4768SWKM](/sequence-files/IGVFFI4768SWKM/), [IGVFFI3608NARM](/sequence-files/IGVFFI3608NARM/), [IGVFFI5026SMOZ](/sequence-files/IGVFFI5026SMOZ/), [IGVFFI9977TUTV](/sequence-files/IGVFFI9977TUTV/), [IGVFFI4668KNFM](/sequence-files/IGVFFI4668KNFM/), [IGVFFI9245YSJZ](/sequence-files/IGVFFI9245YSJZ/), [IGVFFI2274LJGY](/sequence-files/IGVFFI2274LJGY/), [IGVFFI7261BCWU](/sequence-files/IGVFFI7261BCWU/), [IGVFFI0591PYBE](/sequence-files/IGVFFI0591PYBE/), [IGVFFI2635SYNR](/sequence-files/IGVFFI2635SYNR/), [IGVFFI3864TQJZ](/sequence-files/IGVFFI3864TQJZ/), [IGVFFI4749WIDM](/sequence-files/IGVFFI4749WIDM/), [IGVFFI3959KSBT](/sequence-files/IGVFFI3959KSBT/), [IGVFFI9519UJYB](/sequence-files/IGVFFI9519UJYB/), [IGVFFI6088TMDI](/sequence-files/IGVFFI6088TMDI/), [IGVFFI9638EHWU](/sequence-files/IGVFFI9638EHWU/), [IGVFFI9072QHYO](/sequence-files/IGVFFI9072QHYO/), [IGVFFI0716CEDA](/sequence-files/IGVFFI0716CEDA/), [IGVFFI2599SAGS](/sequence-files/IGVFFI2599SAGS/), [IGVFFI8433XXEH](/sequence-files/IGVFFI8433XXEH/), [IGVFFI4575MKMG](/sequence-files/IGVFFI4575MKMG/), [IGVFFI2212DXMY](/sequence-files/IGVFFI2212DXMY/), [IGVFFI3046HDXB](/sequence-files/IGVFFI3046HDXB/), [IGVFFI8695QQHR](/sequence-files/IGVFFI8695QQHR/) 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/IGVFDS7133IGCV/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7133IGCV](/auxiliary-sets/IGVFDS7133IGCV/) has sequence file(s) [IGVFFI1368LSCJ](/sequence-files/IGVFFI1368LSCJ/), [IGVFFI6696BZYA](/sequence-files/IGVFFI6696BZYA/), [IGVFFI9305KZOV](/sequence-files/IGVFFI9305KZOV/), [IGVFFI1085QHKS](/sequence-files/IGVFFI1085QHKS/), [IGVFFI4908VVVZ](/sequence-files/IGVFFI4908VVVZ/), [IGVFFI1621EULU](/sequence-files/IGVFFI1621EULU/), [IGVFFI4297AHZA](/sequence-files/IGVFFI4297AHZA/), [IGVFFI1446IIUH](/sequence-files/IGVFFI1446IIUH/), [IGVFFI1131DQUS](/sequence-files/IGVFFI1131DQUS/), [IGVFFI4165XEYG](/sequence-files/IGVFFI4165XEYG/), [IGVFFI9459ZYJC](/sequence-files/IGVFFI9459ZYJC/), [IGVFFI2891JOLR](/sequence-files/IGVFFI2891JOLR/), [IGVFFI7951MGOG](/sequence-files/IGVFFI7951MGOG/), [IGVFFI9417QZSJ](/sequence-files/IGVFFI9417QZSJ/), [IGVFFI2771VDEV](/sequence-files/IGVFFI2771VDEV/), [IGVFFI1672XROW](/sequence-files/IGVFFI1672XROW/), [IGVFFI5251WUBT](/sequence-files/IGVFFI5251WUBT/), [IGVFFI2393SXQP](/sequence-files/IGVFFI2393SXQP/), [IGVFFI2535BTAI](/sequence-files/IGVFFI2535BTAI/), [IGVFFI1696NTIX](/sequence-files/IGVFFI1696NTIX/), [IGVFFI0025YWDI](/sequence-files/IGVFFI0025YWDI/), [IGVFFI8725MRSD](/sequence-files/IGVFFI8725MRSD/), [IGVFFI2968SOPK](/sequence-files/IGVFFI2968SOPK/), [IGVFFI3021EADH](/sequence-files/IGVFFI3021EADH/), [IGVFFI4768SWKM](/sequence-files/IGVFFI4768SWKM/), [IGVFFI3608NARM](/sequence-files/IGVFFI3608NARM/), [IGVFFI5026SMOZ](/sequence-files/IGVFFI5026SMOZ/), [IGVFFI9977TUTV](/sequence-files/IGVFFI9977TUTV/), [IGVFFI4668KNFM](/sequence-files/IGVFFI4668KNFM/), [IGVFFI9245YSJZ](/sequence-files/IGVFFI9245YSJZ/), [IGVFFI2274LJGY](/sequence-files/IGVFFI2274LJGY/), [IGVFFI7261BCWU](/sequence-files/IGVFFI7261BCWU/), [IGVFFI0591PYBE](/sequence-files/IGVFFI0591PYBE/), [IGVFFI2635SYNR](/sequence-files/IGVFFI2635SYNR/), [IGVFFI3864TQJZ](/sequence-files/IGVFFI3864TQJZ/), [IGVFFI4749WIDM](/sequence-files/IGVFFI4749WIDM/), [IGVFFI3959KSBT](/sequence-files/IGVFFI3959KSBT/), [IGVFFI9519UJYB](/sequence-files/IGVFFI9519UJYB/), [IGVFFI6088TMDI](/sequence-files/IGVFFI6088TMDI/), [IGVFFI9638EHWU](/sequence-files/IGVFFI9638EHWU/), [IGVFFI9072QHYO](/sequence-files/IGVFFI9072QHYO/), [IGVFFI0716CEDA](/sequence-files/IGVFFI0716CEDA/), [IGVFFI2599SAGS](/sequence-files/IGVFFI2599SAGS/), [IGVFFI8433XXEH](/sequence-files/IGVFFI8433XXEH/), [IGVFFI4575MKMG](/sequence-files/IGVFFI4575MKMG/), [IGVFFI2212DXMY](/sequence-files/IGVFFI2212DXMY/), [IGVFFI3046HDXB](/sequence-files/IGVFFI3046HDXB/), [IGVFFI8695QQHR](/sequence-files/IGVFFI8695QQHR/) 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/IGVFDS7133IGCV/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7133IGCV](/auxiliary-sets/IGVFDS7133IGCV/) 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/IGVFDS7133IGCV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7133IGCV/",
"accession": "IGVFDS7133IGCV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-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": "2023-11-30T22:49:10.648698+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": "2023-12-20T23:06:00.159385+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9470HNZI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9470HNZI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-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": "2023-12-05T21:56:37.689269+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": "0f5d693f-567c-42ee-8d33-2ece5447d4a5"
}