{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6566NSFE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6566NSFE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-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 measurement set [IGVFDS6566NSFE](/measurement-sets/IGVFDS6566NSFE/) has in progress subobject auxiliary set [IGVFDS8118YVBF](/auxiliary-sets/IGVFDS8118YVBF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6566NSFE/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2408BZVR](/in-vitro-systems/IGVFSM2408BZVR/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM2408BZVR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8118YVBF](/auxiliary-sets/IGVFDS8118YVBF/) has sequence file(s): [IGVFFI4204RLVH](/sequence-files/IGVFFI4204RLVH/), [IGVFFI2984EDTY](/sequence-files/IGVFFI2984EDTY/), [IGVFFI5726LPFH](/sequence-files/IGVFFI5726LPFH/), [IGVFFI0244IBMM](/sequence-files/IGVFFI0244IBMM/), [IGVFFI7678AHJC](/sequence-files/IGVFFI7678AHJC/), [IGVFFI7933FCWL](/sequence-files/IGVFFI7933FCWL/), [IGVFFI4732PEHO](/sequence-files/IGVFFI4732PEHO/), [IGVFFI6164WCXK](/sequence-files/IGVFFI6164WCXK/), [IGVFFI9067TAZJ](/sequence-files/IGVFFI9067TAZJ/), [IGVFFI1513OYSZ](/sequence-files/IGVFFI1513OYSZ/), [IGVFFI8225XZCT](/sequence-files/IGVFFI8225XZCT/), [IGVFFI1798YKOA](/sequence-files/IGVFFI1798YKOA/), [IGVFFI8743MIDD](/sequence-files/IGVFFI8743MIDD/), [IGVFFI8571BPNW](/sequence-files/IGVFFI8571BPNW/), [IGVFFI0003APOI](/sequence-files/IGVFFI0003APOI/), [IGVFFI4953PHGA](/sequence-files/IGVFFI4953PHGA/), [IGVFFI6563TIPW](/sequence-files/IGVFFI6563TIPW/), [IGVFFI1476WRAJ](/sequence-files/IGVFFI1476WRAJ/), [IGVFFI7380MXEA](/sequence-files/IGVFFI7380MXEA/), [IGVFFI2861IEVB](/sequence-files/IGVFFI2861IEVB/), [IGVFFI0848OOOE](/sequence-files/IGVFFI0848OOOE/), [IGVFFI3819OAYR](/sequence-files/IGVFFI3819OAYR/), [IGVFFI2311WTMC](/sequence-files/IGVFFI2311WTMC/), [IGVFFI2724HCRI](/sequence-files/IGVFFI2724HCRI/), [IGVFFI8708JEZC](/sequence-files/IGVFFI8708JEZC/), [IGVFFI9651WZLO](/sequence-files/IGVFFI9651WZLO/), [IGVFFI2365GBAH](/sequence-files/IGVFFI2365GBAH/), [IGVFFI4236NVNA](/sequence-files/IGVFFI4236NVNA/), [IGVFFI0370AJYV](/sequence-files/IGVFFI0370AJYV/), [IGVFFI9535KNGY](/sequence-files/IGVFFI9535KNGY/), [IGVFFI1471BOIM](/sequence-files/IGVFFI1471BOIM/), [IGVFFI7879HYJU](/sequence-files/IGVFFI7879HYJU/), [IGVFFI3033UQWK](/sequence-files/IGVFFI3033UQWK/), [IGVFFI8049GRXH](/sequence-files/IGVFFI8049GRXH/), [IGVFFI7598TPHN](/sequence-files/IGVFFI7598TPHN/), [IGVFFI6569SGYE](/sequence-files/IGVFFI6569SGYE/), [IGVFFI3080XNXA](/sequence-files/IGVFFI3080XNXA/), [IGVFFI5990NXWI](/sequence-files/IGVFFI5990NXWI/), [IGVFFI4248IZHB](/sequence-files/IGVFFI4248IZHB/), [IGVFFI6205ICKZ](/sequence-files/IGVFFI6205ICKZ/), [IGVFFI4757SUFX](/sequence-files/IGVFFI4757SUFX/), [IGVFFI4923RXZB](/sequence-files/IGVFFI4923RXZB/), [IGVFFI1121LZKZ](/sequence-files/IGVFFI1121LZKZ/), [IGVFFI7201BARU](/sequence-files/IGVFFI7201BARU/), [IGVFFI2631IOKE](/sequence-files/IGVFFI2631IOKE/), [IGVFFI2367JYCH](/sequence-files/IGVFFI2367JYCH/), [IGVFFI9388RYCH](/sequence-files/IGVFFI9388RYCH/), [IGVFFI7758ZQWU](/sequence-files/IGVFFI7758ZQWU/) 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/IGVFDS8118YVBF/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6566NSFE](/measurement-sets/IGVFDS6566NSFE/) 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/IGVFDS6566NSFE/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8118YVBF](/auxiliary-sets/IGVFDS8118YVBF/) has sequence file(s) [IGVFFI4204RLVH](/sequence-files/IGVFFI4204RLVH/), [IGVFFI2984EDTY](/sequence-files/IGVFFI2984EDTY/), [IGVFFI5726LPFH](/sequence-files/IGVFFI5726LPFH/), [IGVFFI0244IBMM](/sequence-files/IGVFFI0244IBMM/), [IGVFFI7678AHJC](/sequence-files/IGVFFI7678AHJC/), [IGVFFI7933FCWL](/sequence-files/IGVFFI7933FCWL/), [IGVFFI4732PEHO](/sequence-files/IGVFFI4732PEHO/), [IGVFFI6164WCXK](/sequence-files/IGVFFI6164WCXK/), [IGVFFI9067TAZJ](/sequence-files/IGVFFI9067TAZJ/), [IGVFFI1513OYSZ](/sequence-files/IGVFFI1513OYSZ/), [IGVFFI8225XZCT](/sequence-files/IGVFFI8225XZCT/), [IGVFFI1798YKOA](/sequence-files/IGVFFI1798YKOA/), [IGVFFI8743MIDD](/sequence-files/IGVFFI8743MIDD/), [IGVFFI8571BPNW](/sequence-files/IGVFFI8571BPNW/), [IGVFFI0003APOI](/sequence-files/IGVFFI0003APOI/), [IGVFFI4953PHGA](/sequence-files/IGVFFI4953PHGA/), [IGVFFI6563TIPW](/sequence-files/IGVFFI6563TIPW/), [IGVFFI1476WRAJ](/sequence-files/IGVFFI1476WRAJ/), [IGVFFI7380MXEA](/sequence-files/IGVFFI7380MXEA/), [IGVFFI2861IEVB](/sequence-files/IGVFFI2861IEVB/), [IGVFFI0848OOOE](/sequence-files/IGVFFI0848OOOE/), [IGVFFI3819OAYR](/sequence-files/IGVFFI3819OAYR/), [IGVFFI2311WTMC](/sequence-files/IGVFFI2311WTMC/), [IGVFFI2724HCRI](/sequence-files/IGVFFI2724HCRI/), [IGVFFI8708JEZC](/sequence-files/IGVFFI8708JEZC/), [IGVFFI9651WZLO](/sequence-files/IGVFFI9651WZLO/), [IGVFFI2365GBAH](/sequence-files/IGVFFI2365GBAH/), [IGVFFI4236NVNA](/sequence-files/IGVFFI4236NVNA/), [IGVFFI0370AJYV](/sequence-files/IGVFFI0370AJYV/), [IGVFFI9535KNGY](/sequence-files/IGVFFI9535KNGY/), [IGVFFI1471BOIM](/sequence-files/IGVFFI1471BOIM/), [IGVFFI7879HYJU](/sequence-files/IGVFFI7879HYJU/), [IGVFFI3033UQWK](/sequence-files/IGVFFI3033UQWK/), [IGVFFI8049GRXH](/sequence-files/IGVFFI8049GRXH/), [IGVFFI7598TPHN](/sequence-files/IGVFFI7598TPHN/), [IGVFFI6569SGYE](/sequence-files/IGVFFI6569SGYE/), [IGVFFI3080XNXA](/sequence-files/IGVFFI3080XNXA/), [IGVFFI5990NXWI](/sequence-files/IGVFFI5990NXWI/), [IGVFFI4248IZHB](/sequence-files/IGVFFI4248IZHB/), [IGVFFI6205ICKZ](/sequence-files/IGVFFI6205ICKZ/), [IGVFFI4757SUFX](/sequence-files/IGVFFI4757SUFX/), [IGVFFI4923RXZB](/sequence-files/IGVFFI4923RXZB/), [IGVFFI1121LZKZ](/sequence-files/IGVFFI1121LZKZ/), [IGVFFI7201BARU](/sequence-files/IGVFFI7201BARU/), [IGVFFI2631IOKE](/sequence-files/IGVFFI2631IOKE/), [IGVFFI2367JYCH](/sequence-files/IGVFFI2367JYCH/), [IGVFFI9388RYCH](/sequence-files/IGVFFI9388RYCH/), [IGVFFI7758ZQWU](/sequence-files/IGVFFI7758ZQWU/) 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/IGVFDS8118YVBF/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8118YVBF](/auxiliary-sets/IGVFDS8118YVBF/) 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/IGVFDS8118YVBF/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8118YVBF/",
"accession": "IGVFDS8118YVBF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:54.841629+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:05:38.410525+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2408BZVR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2408BZVR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 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": "2023-12-05T21:47:22.625396+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": "0a9b802d-7ea7-42dd-90a3-61b398babdf6"
}