{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2840EKZI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2840EKZI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-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 [IGVFSM6618IGOS](/in-vitro-systems/IGVFSM6618IGOS/) 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/IGVFSM6618IGOS/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2840EKZI](/measurement-sets/IGVFDS2840EKZI/) has in progress subobject auxiliary set [IGVFDS4925CUTK](/auxiliary-sets/IGVFDS4925CUTK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2840EKZI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4925CUTK](/auxiliary-sets/IGVFDS4925CUTK/) has sequence file(s): [IGVFFI1880PLDA](/sequence-files/IGVFFI1880PLDA/), [IGVFFI3501JYBV](/sequence-files/IGVFFI3501JYBV/), [IGVFFI2388IZTL](/sequence-files/IGVFFI2388IZTL/), [IGVFFI7338SXVG](/sequence-files/IGVFFI7338SXVG/), [IGVFFI0800XMRX](/sequence-files/IGVFFI0800XMRX/), [IGVFFI6986UGWD](/sequence-files/IGVFFI6986UGWD/), [IGVFFI9705BHNF](/sequence-files/IGVFFI9705BHNF/), [IGVFFI3120KSDW](/sequence-files/IGVFFI3120KSDW/), [IGVFFI8362ATFS](/sequence-files/IGVFFI8362ATFS/), [IGVFFI3930ZOWK](/sequence-files/IGVFFI3930ZOWK/), [IGVFFI1302KPOP](/sequence-files/IGVFFI1302KPOP/), [IGVFFI3611PDCW](/sequence-files/IGVFFI3611PDCW/), [IGVFFI8938LHYF](/sequence-files/IGVFFI8938LHYF/), [IGVFFI0560VGRG](/sequence-files/IGVFFI0560VGRG/), [IGVFFI5052LQEQ](/sequence-files/IGVFFI5052LQEQ/), [IGVFFI8428LUMF](/sequence-files/IGVFFI8428LUMF/), [IGVFFI5275PFJX](/sequence-files/IGVFFI5275PFJX/), [IGVFFI4418LEXH](/sequence-files/IGVFFI4418LEXH/), [IGVFFI4900SGGG](/sequence-files/IGVFFI4900SGGG/), [IGVFFI0334XULB](/sequence-files/IGVFFI0334XULB/), [IGVFFI2670BBNP](/sequence-files/IGVFFI2670BBNP/), [IGVFFI5631FGZL](/sequence-files/IGVFFI5631FGZL/), [IGVFFI3855TMQP](/sequence-files/IGVFFI3855TMQP/), [IGVFFI5538XZUE](/sequence-files/IGVFFI5538XZUE/), [IGVFFI5194SJJM](/sequence-files/IGVFFI5194SJJM/), [IGVFFI9343NCCM](/sequence-files/IGVFFI9343NCCM/), [IGVFFI3043TMDH](/sequence-files/IGVFFI3043TMDH/), [IGVFFI7497BWQL](/sequence-files/IGVFFI7497BWQL/), [IGVFFI7936TMWF](/sequence-files/IGVFFI7936TMWF/), [IGVFFI9560GGIR](/sequence-files/IGVFFI9560GGIR/), [IGVFFI8427AOJM](/sequence-files/IGVFFI8427AOJM/), [IGVFFI3612VVSP](/sequence-files/IGVFFI3612VVSP/), [IGVFFI2381WRZI](/sequence-files/IGVFFI2381WRZI/), [IGVFFI7307WOQE](/sequence-files/IGVFFI7307WOQE/), [IGVFFI2166XOMZ](/sequence-files/IGVFFI2166XOMZ/), [IGVFFI0794GHTL](/sequence-files/IGVFFI0794GHTL/), [IGVFFI0164OREL](/sequence-files/IGVFFI0164OREL/), [IGVFFI2901MLSA](/sequence-files/IGVFFI2901MLSA/), [IGVFFI9824XZLY](/sequence-files/IGVFFI9824XZLY/), [IGVFFI9673CGUQ](/sequence-files/IGVFFI9673CGUQ/), [IGVFFI5022KHTB](/sequence-files/IGVFFI5022KHTB/), [IGVFFI1144SIWW](/sequence-files/IGVFFI1144SIWW/), [IGVFFI1182QGFY](/sequence-files/IGVFFI1182QGFY/), [IGVFFI9344DUYZ](/sequence-files/IGVFFI9344DUYZ/), [IGVFFI3204WWUO](/sequence-files/IGVFFI3204WWUO/), [IGVFFI7401ZKTG](/sequence-files/IGVFFI7401ZKTG/), [IGVFFI9743FXHS](/sequence-files/IGVFFI9743FXHS/), [IGVFFI5261TGLF](/sequence-files/IGVFFI5261TGLF/) 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/IGVFDS4925CUTK/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2840EKZI](/measurement-sets/IGVFDS2840EKZI/) 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/IGVFDS2840EKZI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4925CUTK](/auxiliary-sets/IGVFDS4925CUTK/) has sequence file(s) [IGVFFI1880PLDA](/sequence-files/IGVFFI1880PLDA/), [IGVFFI3501JYBV](/sequence-files/IGVFFI3501JYBV/), [IGVFFI2388IZTL](/sequence-files/IGVFFI2388IZTL/), [IGVFFI7338SXVG](/sequence-files/IGVFFI7338SXVG/), [IGVFFI0800XMRX](/sequence-files/IGVFFI0800XMRX/), [IGVFFI6986UGWD](/sequence-files/IGVFFI6986UGWD/), [IGVFFI9705BHNF](/sequence-files/IGVFFI9705BHNF/), [IGVFFI3120KSDW](/sequence-files/IGVFFI3120KSDW/), [IGVFFI8362ATFS](/sequence-files/IGVFFI8362ATFS/), [IGVFFI3930ZOWK](/sequence-files/IGVFFI3930ZOWK/), [IGVFFI1302KPOP](/sequence-files/IGVFFI1302KPOP/), [IGVFFI3611PDCW](/sequence-files/IGVFFI3611PDCW/), [IGVFFI8938LHYF](/sequence-files/IGVFFI8938LHYF/), [IGVFFI0560VGRG](/sequence-files/IGVFFI0560VGRG/), [IGVFFI5052LQEQ](/sequence-files/IGVFFI5052LQEQ/), [IGVFFI8428LUMF](/sequence-files/IGVFFI8428LUMF/), [IGVFFI5275PFJX](/sequence-files/IGVFFI5275PFJX/), [IGVFFI4418LEXH](/sequence-files/IGVFFI4418LEXH/), [IGVFFI4900SGGG](/sequence-files/IGVFFI4900SGGG/), [IGVFFI0334XULB](/sequence-files/IGVFFI0334XULB/), [IGVFFI2670BBNP](/sequence-files/IGVFFI2670BBNP/), [IGVFFI5631FGZL](/sequence-files/IGVFFI5631FGZL/), [IGVFFI3855TMQP](/sequence-files/IGVFFI3855TMQP/), [IGVFFI5538XZUE](/sequence-files/IGVFFI5538XZUE/), [IGVFFI5194SJJM](/sequence-files/IGVFFI5194SJJM/), [IGVFFI9343NCCM](/sequence-files/IGVFFI9343NCCM/), [IGVFFI3043TMDH](/sequence-files/IGVFFI3043TMDH/), [IGVFFI7497BWQL](/sequence-files/IGVFFI7497BWQL/), [IGVFFI7936TMWF](/sequence-files/IGVFFI7936TMWF/), [IGVFFI9560GGIR](/sequence-files/IGVFFI9560GGIR/), [IGVFFI8427AOJM](/sequence-files/IGVFFI8427AOJM/), [IGVFFI3612VVSP](/sequence-files/IGVFFI3612VVSP/), [IGVFFI2381WRZI](/sequence-files/IGVFFI2381WRZI/), [IGVFFI7307WOQE](/sequence-files/IGVFFI7307WOQE/), [IGVFFI2166XOMZ](/sequence-files/IGVFFI2166XOMZ/), [IGVFFI0794GHTL](/sequence-files/IGVFFI0794GHTL/), [IGVFFI0164OREL](/sequence-files/IGVFFI0164OREL/), [IGVFFI2901MLSA](/sequence-files/IGVFFI2901MLSA/), [IGVFFI9824XZLY](/sequence-files/IGVFFI9824XZLY/), [IGVFFI9673CGUQ](/sequence-files/IGVFFI9673CGUQ/), [IGVFFI5022KHTB](/sequence-files/IGVFFI5022KHTB/), [IGVFFI1144SIWW](/sequence-files/IGVFFI1144SIWW/), [IGVFFI1182QGFY](/sequence-files/IGVFFI1182QGFY/), [IGVFFI9344DUYZ](/sequence-files/IGVFFI9344DUYZ/), [IGVFFI3204WWUO](/sequence-files/IGVFFI3204WWUO/), [IGVFFI7401ZKTG](/sequence-files/IGVFFI7401ZKTG/), [IGVFFI9743FXHS](/sequence-files/IGVFFI9743FXHS/), [IGVFFI5261TGLF](/sequence-files/IGVFFI5261TGLF/) 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/IGVFDS4925CUTK/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4925CUTK](/auxiliary-sets/IGVFDS4925CUTK/) 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/IGVFDS4925CUTK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4925CUTK/",
"accession": "IGVFDS4925CUTK",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:13.823250+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": "2023-12-20T23:08:30.324162+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6618IGOS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6618IGOS",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep2-FFrep3-BinC"
],
"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 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": "2023-12-13T10:16:41.728005+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": "1a5097e9-01f5-437a-8b88-12e5fd8acfa9"
}