{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8933DNXM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8933DNXM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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 measurement set [IGVFDS8933DNXM](/measurement-sets/IGVFDS8933DNXM/) has in progress subobject auxiliary set [IGVFDS5696LHVW](/auxiliary-sets/IGVFDS5696LHVW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8933DNXM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4794HUBP](/in-vitro-systems/IGVFSM4794HUBP/) 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/IGVFSM4794HUBP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8933DNXM](/measurement-sets/IGVFDS8933DNXM/) 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/IGVFDS8933DNXM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5696LHVW](/auxiliary-sets/IGVFDS5696LHVW/) has sequence file(s): [IGVFFI2238CARU](/sequence-files/IGVFFI2238CARU/), [IGVFFI3702YEDC](/sequence-files/IGVFFI3702YEDC/), [IGVFFI1630JZAD](/sequence-files/IGVFFI1630JZAD/), [IGVFFI7558RNVD](/sequence-files/IGVFFI7558RNVD/), [IGVFFI1585ZQJE](/sequence-files/IGVFFI1585ZQJE/), [IGVFFI1213FSIK](/sequence-files/IGVFFI1213FSIK/), [IGVFFI3487DZFK](/sequence-files/IGVFFI3487DZFK/), [IGVFFI9563ERPL](/sequence-files/IGVFFI9563ERPL/), [IGVFFI3648JBVF](/sequence-files/IGVFFI3648JBVF/), [IGVFFI4686FYKM](/sequence-files/IGVFFI4686FYKM/), [IGVFFI8511TJIJ](/sequence-files/IGVFFI8511TJIJ/), [IGVFFI7581RVPX](/sequence-files/IGVFFI7581RVPX/), [IGVFFI6187MGNZ](/sequence-files/IGVFFI6187MGNZ/), [IGVFFI0209SARS](/sequence-files/IGVFFI0209SARS/), [IGVFFI4519DJCW](/sequence-files/IGVFFI4519DJCW/), [IGVFFI4630LIUQ](/sequence-files/IGVFFI4630LIUQ/), [IGVFFI3888NJTZ](/sequence-files/IGVFFI3888NJTZ/), [IGVFFI3403EWWS](/sequence-files/IGVFFI3403EWWS/), [IGVFFI0347SWVK](/sequence-files/IGVFFI0347SWVK/), [IGVFFI3694TTRC](/sequence-files/IGVFFI3694TTRC/), [IGVFFI9527NMCV](/sequence-files/IGVFFI9527NMCV/), [IGVFFI9422MVLA](/sequence-files/IGVFFI9422MVLA/), [IGVFFI2826YXET](/sequence-files/IGVFFI2826YXET/), [IGVFFI9420WWVZ](/sequence-files/IGVFFI9420WWVZ/), [IGVFFI9949ISLU](/sequence-files/IGVFFI9949ISLU/), [IGVFFI1099MOSE](/sequence-files/IGVFFI1099MOSE/), [IGVFFI9305KPWP](/sequence-files/IGVFFI9305KPWP/), [IGVFFI7078XVGU](/sequence-files/IGVFFI7078XVGU/), [IGVFFI0119IRJN](/sequence-files/IGVFFI0119IRJN/), [IGVFFI5982LQBN](/sequence-files/IGVFFI5982LQBN/), [IGVFFI1489BTPJ](/sequence-files/IGVFFI1489BTPJ/), [IGVFFI9167DMLX](/sequence-files/IGVFFI9167DMLX/), [IGVFFI1262CNBY](/sequence-files/IGVFFI1262CNBY/), [IGVFFI6188KDSO](/sequence-files/IGVFFI6188KDSO/), [IGVFFI6909WEPF](/sequence-files/IGVFFI6909WEPF/), [IGVFFI9631TQQE](/sequence-files/IGVFFI9631TQQE/), [IGVFFI6158IGNG](/sequence-files/IGVFFI6158IGNG/), [IGVFFI1134BMHN](/sequence-files/IGVFFI1134BMHN/), [IGVFFI1317WDCE](/sequence-files/IGVFFI1317WDCE/), [IGVFFI6891NPRP](/sequence-files/IGVFFI6891NPRP/), [IGVFFI7976UOJV](/sequence-files/IGVFFI7976UOJV/), [IGVFFI0547MOLV](/sequence-files/IGVFFI0547MOLV/), [IGVFFI6395FYBC](/sequence-files/IGVFFI6395FYBC/), [IGVFFI4175TOFI](/sequence-files/IGVFFI4175TOFI/), [IGVFFI6355MUWD](/sequence-files/IGVFFI6355MUWD/), [IGVFFI2400UDCF](/sequence-files/IGVFFI2400UDCF/), [IGVFFI6775QZZY](/sequence-files/IGVFFI6775QZZY/), [IGVFFI0665LKTR](/sequence-files/IGVFFI0665LKTR/) 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/IGVFDS5696LHVW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5696LHVW](/auxiliary-sets/IGVFDS5696LHVW/) has sequence file(s) [IGVFFI2238CARU](/sequence-files/IGVFFI2238CARU/), [IGVFFI3702YEDC](/sequence-files/IGVFFI3702YEDC/), [IGVFFI1630JZAD](/sequence-files/IGVFFI1630JZAD/), [IGVFFI7558RNVD](/sequence-files/IGVFFI7558RNVD/), [IGVFFI1585ZQJE](/sequence-files/IGVFFI1585ZQJE/), [IGVFFI1213FSIK](/sequence-files/IGVFFI1213FSIK/), [IGVFFI3487DZFK](/sequence-files/IGVFFI3487DZFK/), [IGVFFI9563ERPL](/sequence-files/IGVFFI9563ERPL/), [IGVFFI3648JBVF](/sequence-files/IGVFFI3648JBVF/), [IGVFFI4686FYKM](/sequence-files/IGVFFI4686FYKM/), [IGVFFI8511TJIJ](/sequence-files/IGVFFI8511TJIJ/), [IGVFFI7581RVPX](/sequence-files/IGVFFI7581RVPX/), [IGVFFI6187MGNZ](/sequence-files/IGVFFI6187MGNZ/), [IGVFFI0209SARS](/sequence-files/IGVFFI0209SARS/), [IGVFFI4519DJCW](/sequence-files/IGVFFI4519DJCW/), [IGVFFI4630LIUQ](/sequence-files/IGVFFI4630LIUQ/), [IGVFFI3888NJTZ](/sequence-files/IGVFFI3888NJTZ/), [IGVFFI3403EWWS](/sequence-files/IGVFFI3403EWWS/), [IGVFFI0347SWVK](/sequence-files/IGVFFI0347SWVK/), [IGVFFI3694TTRC](/sequence-files/IGVFFI3694TTRC/), [IGVFFI9527NMCV](/sequence-files/IGVFFI9527NMCV/), [IGVFFI9422MVLA](/sequence-files/IGVFFI9422MVLA/), [IGVFFI2826YXET](/sequence-files/IGVFFI2826YXET/), [IGVFFI9420WWVZ](/sequence-files/IGVFFI9420WWVZ/), [IGVFFI9949ISLU](/sequence-files/IGVFFI9949ISLU/), [IGVFFI1099MOSE](/sequence-files/IGVFFI1099MOSE/), [IGVFFI9305KPWP](/sequence-files/IGVFFI9305KPWP/), [IGVFFI7078XVGU](/sequence-files/IGVFFI7078XVGU/), [IGVFFI0119IRJN](/sequence-files/IGVFFI0119IRJN/), [IGVFFI5982LQBN](/sequence-files/IGVFFI5982LQBN/), [IGVFFI1489BTPJ](/sequence-files/IGVFFI1489BTPJ/), [IGVFFI9167DMLX](/sequence-files/IGVFFI9167DMLX/), [IGVFFI1262CNBY](/sequence-files/IGVFFI1262CNBY/), [IGVFFI6188KDSO](/sequence-files/IGVFFI6188KDSO/), [IGVFFI6909WEPF](/sequence-files/IGVFFI6909WEPF/), [IGVFFI9631TQQE](/sequence-files/IGVFFI9631TQQE/), [IGVFFI6158IGNG](/sequence-files/IGVFFI6158IGNG/), [IGVFFI1134BMHN](/sequence-files/IGVFFI1134BMHN/), [IGVFFI1317WDCE](/sequence-files/IGVFFI1317WDCE/), [IGVFFI6891NPRP](/sequence-files/IGVFFI6891NPRP/), [IGVFFI7976UOJV](/sequence-files/IGVFFI7976UOJV/), [IGVFFI0547MOLV](/sequence-files/IGVFFI0547MOLV/), [IGVFFI6395FYBC](/sequence-files/IGVFFI6395FYBC/), [IGVFFI4175TOFI](/sequence-files/IGVFFI4175TOFI/), [IGVFFI6355MUWD](/sequence-files/IGVFFI6355MUWD/), [IGVFFI2400UDCF](/sequence-files/IGVFFI2400UDCF/), [IGVFFI6775QZZY](/sequence-files/IGVFFI6775QZZY/), [IGVFFI0665LKTR](/sequence-files/IGVFFI0665LKTR/) 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/IGVFDS5696LHVW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5696LHVW](/auxiliary-sets/IGVFDS5696LHVW/) 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/IGVFDS5696LHVW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5696LHVW/",
"accession": "IGVFDS5696LHVW",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:40.287150+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/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:47.018050+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4794HUBP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4794HUBP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinB"
],
"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_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": "2023-12-13T08:33:43.902345+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": "bfd8e3ec-98a2-476f-a0f0-bb2426717803"
}