{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3485SAPD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3485SAPD",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_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 measurement set [IGVFDS3485SAPD](/measurement-sets/IGVFDS3485SAPD/) has in progress subobject auxiliary set [IGVFDS6063TTCA](/auxiliary-sets/IGVFDS6063TTCA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3485SAPD/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1740AUMH](/in-vitro-systems/IGVFSM1740AUMH/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM1740AUMH/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6063TTCA](/auxiliary-sets/IGVFDS6063TTCA/) has sequence file(s): [IGVFFI6868ZIZU](/sequence-files/IGVFFI6868ZIZU/), [IGVFFI9743LUOW](/sequence-files/IGVFFI9743LUOW/), [IGVFFI4319GMWE](/sequence-files/IGVFFI4319GMWE/), [IGVFFI7798HOHF](/sequence-files/IGVFFI7798HOHF/), [IGVFFI2221GABI](/sequence-files/IGVFFI2221GABI/), [IGVFFI4966HGLS](/sequence-files/IGVFFI4966HGLS/), [IGVFFI4457HWQJ](/sequence-files/IGVFFI4457HWQJ/), [IGVFFI4183BLYM](/sequence-files/IGVFFI4183BLYM/), [IGVFFI6265AVEW](/sequence-files/IGVFFI6265AVEW/), [IGVFFI9216PYYG](/sequence-files/IGVFFI9216PYYG/), [IGVFFI1721AWTM](/sequence-files/IGVFFI1721AWTM/), [IGVFFI8885BTAU](/sequence-files/IGVFFI8885BTAU/), [IGVFFI6599FITT](/sequence-files/IGVFFI6599FITT/), [IGVFFI9553ZPOP](/sequence-files/IGVFFI9553ZPOP/), [IGVFFI0886PBVO](/sequence-files/IGVFFI0886PBVO/), [IGVFFI3737WHNM](/sequence-files/IGVFFI3737WHNM/), [IGVFFI2215YSMB](/sequence-files/IGVFFI2215YSMB/), [IGVFFI9635NZHA](/sequence-files/IGVFFI9635NZHA/), [IGVFFI0953CGQB](/sequence-files/IGVFFI0953CGQB/), [IGVFFI7342HLPV](/sequence-files/IGVFFI7342HLPV/), [IGVFFI4811XJFY](/sequence-files/IGVFFI4811XJFY/), [IGVFFI9942BLFG](/sequence-files/IGVFFI9942BLFG/), [IGVFFI3834OCIC](/sequence-files/IGVFFI3834OCIC/), [IGVFFI6588MUBD](/sequence-files/IGVFFI6588MUBD/), [IGVFFI7332SJZD](/sequence-files/IGVFFI7332SJZD/), [IGVFFI4480TAYK](/sequence-files/IGVFFI4480TAYK/), [IGVFFI3784NNIW](/sequence-files/IGVFFI3784NNIW/), [IGVFFI6598PFOW](/sequence-files/IGVFFI6598PFOW/), [IGVFFI8711JENQ](/sequence-files/IGVFFI8711JENQ/), [IGVFFI1951QZWI](/sequence-files/IGVFFI1951QZWI/), [IGVFFI7509ZCDU](/sequence-files/IGVFFI7509ZCDU/), [IGVFFI3129KVKC](/sequence-files/IGVFFI3129KVKC/), [IGVFFI3553ISDU](/sequence-files/IGVFFI3553ISDU/), [IGVFFI1105ARQQ](/sequence-files/IGVFFI1105ARQQ/), [IGVFFI3402XYGE](/sequence-files/IGVFFI3402XYGE/), [IGVFFI5954LMRM](/sequence-files/IGVFFI5954LMRM/), [IGVFFI2228PRWC](/sequence-files/IGVFFI2228PRWC/), [IGVFFI2310WNUI](/sequence-files/IGVFFI2310WNUI/), [IGVFFI3031LCGO](/sequence-files/IGVFFI3031LCGO/), [IGVFFI5351WNRF](/sequence-files/IGVFFI5351WNRF/), [IGVFFI1637MJBF](/sequence-files/IGVFFI1637MJBF/), [IGVFFI3957ZXFV](/sequence-files/IGVFFI3957ZXFV/), [IGVFFI6487WVVT](/sequence-files/IGVFFI6487WVVT/), [IGVFFI5094WSNI](/sequence-files/IGVFFI5094WSNI/), [IGVFFI7133FKPH](/sequence-files/IGVFFI7133FKPH/), [IGVFFI5267FJRZ](/sequence-files/IGVFFI5267FJRZ/), [IGVFFI0369XBXG](/sequence-files/IGVFFI0369XBXG/), [IGVFFI0905GRJE](/sequence-files/IGVFFI0905GRJE/) 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/IGVFDS6063TTCA/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3485SAPD](/measurement-sets/IGVFDS3485SAPD/) 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/IGVFDS3485SAPD/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6063TTCA](/auxiliary-sets/IGVFDS6063TTCA/) has sequence file(s) [IGVFFI6868ZIZU](/sequence-files/IGVFFI6868ZIZU/), [IGVFFI9743LUOW](/sequence-files/IGVFFI9743LUOW/), [IGVFFI4319GMWE](/sequence-files/IGVFFI4319GMWE/), [IGVFFI7798HOHF](/sequence-files/IGVFFI7798HOHF/), [IGVFFI2221GABI](/sequence-files/IGVFFI2221GABI/), [IGVFFI4966HGLS](/sequence-files/IGVFFI4966HGLS/), [IGVFFI4457HWQJ](/sequence-files/IGVFFI4457HWQJ/), [IGVFFI4183BLYM](/sequence-files/IGVFFI4183BLYM/), [IGVFFI6265AVEW](/sequence-files/IGVFFI6265AVEW/), [IGVFFI9216PYYG](/sequence-files/IGVFFI9216PYYG/), [IGVFFI1721AWTM](/sequence-files/IGVFFI1721AWTM/), [IGVFFI8885BTAU](/sequence-files/IGVFFI8885BTAU/), [IGVFFI6599FITT](/sequence-files/IGVFFI6599FITT/), [IGVFFI9553ZPOP](/sequence-files/IGVFFI9553ZPOP/), [IGVFFI0886PBVO](/sequence-files/IGVFFI0886PBVO/), [IGVFFI3737WHNM](/sequence-files/IGVFFI3737WHNM/), [IGVFFI2215YSMB](/sequence-files/IGVFFI2215YSMB/), [IGVFFI9635NZHA](/sequence-files/IGVFFI9635NZHA/), [IGVFFI0953CGQB](/sequence-files/IGVFFI0953CGQB/), [IGVFFI7342HLPV](/sequence-files/IGVFFI7342HLPV/), [IGVFFI4811XJFY](/sequence-files/IGVFFI4811XJFY/), [IGVFFI9942BLFG](/sequence-files/IGVFFI9942BLFG/), [IGVFFI3834OCIC](/sequence-files/IGVFFI3834OCIC/), [IGVFFI6588MUBD](/sequence-files/IGVFFI6588MUBD/), [IGVFFI7332SJZD](/sequence-files/IGVFFI7332SJZD/), [IGVFFI4480TAYK](/sequence-files/IGVFFI4480TAYK/), [IGVFFI3784NNIW](/sequence-files/IGVFFI3784NNIW/), [IGVFFI6598PFOW](/sequence-files/IGVFFI6598PFOW/), [IGVFFI8711JENQ](/sequence-files/IGVFFI8711JENQ/), [IGVFFI1951QZWI](/sequence-files/IGVFFI1951QZWI/), [IGVFFI7509ZCDU](/sequence-files/IGVFFI7509ZCDU/), [IGVFFI3129KVKC](/sequence-files/IGVFFI3129KVKC/), [IGVFFI3553ISDU](/sequence-files/IGVFFI3553ISDU/), [IGVFFI1105ARQQ](/sequence-files/IGVFFI1105ARQQ/), [IGVFFI3402XYGE](/sequence-files/IGVFFI3402XYGE/), [IGVFFI5954LMRM](/sequence-files/IGVFFI5954LMRM/), [IGVFFI2228PRWC](/sequence-files/IGVFFI2228PRWC/), [IGVFFI2310WNUI](/sequence-files/IGVFFI2310WNUI/), [IGVFFI3031LCGO](/sequence-files/IGVFFI3031LCGO/), [IGVFFI5351WNRF](/sequence-files/IGVFFI5351WNRF/), [IGVFFI1637MJBF](/sequence-files/IGVFFI1637MJBF/), [IGVFFI3957ZXFV](/sequence-files/IGVFFI3957ZXFV/), [IGVFFI6487WVVT](/sequence-files/IGVFFI6487WVVT/), [IGVFFI5094WSNI](/sequence-files/IGVFFI5094WSNI/), [IGVFFI7133FKPH](/sequence-files/IGVFFI7133FKPH/), [IGVFFI5267FJRZ](/sequence-files/IGVFFI5267FJRZ/), [IGVFFI0369XBXG](/sequence-files/IGVFFI0369XBXG/), [IGVFFI0905GRJE](/sequence-files/IGVFFI0905GRJE/) 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/IGVFDS6063TTCA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS6063TTCA](/auxiliary-sets/IGVFDS6063TTCA/) 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/IGVFDS6063TTCA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6063TTCA/",
"accession": "IGVFDS6063TTCA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinD_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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:09.216948+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:24.328822+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1740AUMH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1740AUMH",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep4-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% 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": "2023-12-13T09:52:57.879066+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": "6aae81e3-c663-4244-a099-4d23cfbc263e"
}