{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1402WRSD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1402WRSD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_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 [IGVFSM4125CFFV](/in-vitro-systems/IGVFSM4125CFFV/) 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/IGVFSM4125CFFV/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1402WRSD](/measurement-sets/IGVFDS1402WRSD/) has in progress subobject auxiliary set [IGVFDS8995GXYE](/auxiliary-sets/IGVFDS8995GXYE/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1402WRSD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1402WRSD](/measurement-sets/IGVFDS1402WRSD/) 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/IGVFDS1402WRSD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8995GXYE](/auxiliary-sets/IGVFDS8995GXYE/) has sequence file(s): [IGVFFI3349QITO](/sequence-files/IGVFFI3349QITO/), [IGVFFI4041WICZ](/sequence-files/IGVFFI4041WICZ/), [IGVFFI5769PIFS](/sequence-files/IGVFFI5769PIFS/), [IGVFFI8096XEZU](/sequence-files/IGVFFI8096XEZU/), [IGVFFI6721SIJR](/sequence-files/IGVFFI6721SIJR/), [IGVFFI2416XAJS](/sequence-files/IGVFFI2416XAJS/), [IGVFFI4926UHVI](/sequence-files/IGVFFI4926UHVI/), [IGVFFI9425TYGB](/sequence-files/IGVFFI9425TYGB/), [IGVFFI1965IKSP](/sequence-files/IGVFFI1965IKSP/), [IGVFFI8196QMNK](/sequence-files/IGVFFI8196QMNK/), [IGVFFI9446ESYL](/sequence-files/IGVFFI9446ESYL/), [IGVFFI1327TXKF](/sequence-files/IGVFFI1327TXKF/), [IGVFFI7288RHAC](/sequence-files/IGVFFI7288RHAC/), [IGVFFI8009SKVK](/sequence-files/IGVFFI8009SKVK/), [IGVFFI9005AXVA](/sequence-files/IGVFFI9005AXVA/), [IGVFFI1964NANB](/sequence-files/IGVFFI1964NANB/), [IGVFFI7222GUQL](/sequence-files/IGVFFI7222GUQL/), [IGVFFI6018TTVV](/sequence-files/IGVFFI6018TTVV/), [IGVFFI1212NLVW](/sequence-files/IGVFFI1212NLVW/), [IGVFFI5061ILNK](/sequence-files/IGVFFI5061ILNK/), [IGVFFI0079OOSX](/sequence-files/IGVFFI0079OOSX/), [IGVFFI4128OIER](/sequence-files/IGVFFI4128OIER/), [IGVFFI5216WVFP](/sequence-files/IGVFFI5216WVFP/), [IGVFFI7531RCDN](/sequence-files/IGVFFI7531RCDN/), [IGVFFI8171HKOX](/sequence-files/IGVFFI8171HKOX/), [IGVFFI4636EYRQ](/sequence-files/IGVFFI4636EYRQ/), [IGVFFI8986KVVP](/sequence-files/IGVFFI8986KVVP/), [IGVFFI1020MFXK](/sequence-files/IGVFFI1020MFXK/), [IGVFFI3545AWIK](/sequence-files/IGVFFI3545AWIK/), [IGVFFI7447ZCKH](/sequence-files/IGVFFI7447ZCKH/), [IGVFFI0691XYCV](/sequence-files/IGVFFI0691XYCV/), [IGVFFI4580NPDH](/sequence-files/IGVFFI4580NPDH/), [IGVFFI3274PAGO](/sequence-files/IGVFFI3274PAGO/), [IGVFFI2667KWPV](/sequence-files/IGVFFI2667KWPV/), [IGVFFI2567SKQO](/sequence-files/IGVFFI2567SKQO/), [IGVFFI5133ZEUC](/sequence-files/IGVFFI5133ZEUC/), [IGVFFI7813JIXI](/sequence-files/IGVFFI7813JIXI/), [IGVFFI3188XFOG](/sequence-files/IGVFFI3188XFOG/), [IGVFFI3536XWTA](/sequence-files/IGVFFI3536XWTA/), [IGVFFI5932XHJR](/sequence-files/IGVFFI5932XHJR/), [IGVFFI5738NELW](/sequence-files/IGVFFI5738NELW/), [IGVFFI3064NXHF](/sequence-files/IGVFFI3064NXHF/), [IGVFFI9831XTKC](/sequence-files/IGVFFI9831XTKC/), [IGVFFI7657MMEG](/sequence-files/IGVFFI7657MMEG/), [IGVFFI3122LZPJ](/sequence-files/IGVFFI3122LZPJ/), [IGVFFI5457XBYW](/sequence-files/IGVFFI5457XBYW/), [IGVFFI9145VWFH](/sequence-files/IGVFFI9145VWFH/), [IGVFFI8017PIDE](/sequence-files/IGVFFI8017PIDE/) 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/IGVFDS8995GXYE/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8995GXYE](/auxiliary-sets/IGVFDS8995GXYE/) has sequence file(s) [IGVFFI3349QITO](/sequence-files/IGVFFI3349QITO/), [IGVFFI4041WICZ](/sequence-files/IGVFFI4041WICZ/), [IGVFFI5769PIFS](/sequence-files/IGVFFI5769PIFS/), [IGVFFI8096XEZU](/sequence-files/IGVFFI8096XEZU/), [IGVFFI6721SIJR](/sequence-files/IGVFFI6721SIJR/), [IGVFFI2416XAJS](/sequence-files/IGVFFI2416XAJS/), [IGVFFI4926UHVI](/sequence-files/IGVFFI4926UHVI/), [IGVFFI9425TYGB](/sequence-files/IGVFFI9425TYGB/), [IGVFFI1965IKSP](/sequence-files/IGVFFI1965IKSP/), [IGVFFI8196QMNK](/sequence-files/IGVFFI8196QMNK/), [IGVFFI9446ESYL](/sequence-files/IGVFFI9446ESYL/), [IGVFFI1327TXKF](/sequence-files/IGVFFI1327TXKF/), [IGVFFI7288RHAC](/sequence-files/IGVFFI7288RHAC/), [IGVFFI8009SKVK](/sequence-files/IGVFFI8009SKVK/), [IGVFFI9005AXVA](/sequence-files/IGVFFI9005AXVA/), [IGVFFI1964NANB](/sequence-files/IGVFFI1964NANB/), [IGVFFI7222GUQL](/sequence-files/IGVFFI7222GUQL/), [IGVFFI6018TTVV](/sequence-files/IGVFFI6018TTVV/), [IGVFFI1212NLVW](/sequence-files/IGVFFI1212NLVW/), [IGVFFI5061ILNK](/sequence-files/IGVFFI5061ILNK/), [IGVFFI0079OOSX](/sequence-files/IGVFFI0079OOSX/), [IGVFFI4128OIER](/sequence-files/IGVFFI4128OIER/), [IGVFFI5216WVFP](/sequence-files/IGVFFI5216WVFP/), [IGVFFI7531RCDN](/sequence-files/IGVFFI7531RCDN/), [IGVFFI8171HKOX](/sequence-files/IGVFFI8171HKOX/), [IGVFFI4636EYRQ](/sequence-files/IGVFFI4636EYRQ/), [IGVFFI8986KVVP](/sequence-files/IGVFFI8986KVVP/), [IGVFFI1020MFXK](/sequence-files/IGVFFI1020MFXK/), [IGVFFI3545AWIK](/sequence-files/IGVFFI3545AWIK/), [IGVFFI7447ZCKH](/sequence-files/IGVFFI7447ZCKH/), [IGVFFI0691XYCV](/sequence-files/IGVFFI0691XYCV/), [IGVFFI4580NPDH](/sequence-files/IGVFFI4580NPDH/), [IGVFFI3274PAGO](/sequence-files/IGVFFI3274PAGO/), [IGVFFI2667KWPV](/sequence-files/IGVFFI2667KWPV/), [IGVFFI2567SKQO](/sequence-files/IGVFFI2567SKQO/), [IGVFFI5133ZEUC](/sequence-files/IGVFFI5133ZEUC/), [IGVFFI7813JIXI](/sequence-files/IGVFFI7813JIXI/), [IGVFFI3188XFOG](/sequence-files/IGVFFI3188XFOG/), [IGVFFI3536XWTA](/sequence-files/IGVFFI3536XWTA/), [IGVFFI5932XHJR](/sequence-files/IGVFFI5932XHJR/), [IGVFFI5738NELW](/sequence-files/IGVFFI5738NELW/), [IGVFFI3064NXHF](/sequence-files/IGVFFI3064NXHF/), [IGVFFI9831XTKC](/sequence-files/IGVFFI9831XTKC/), [IGVFFI7657MMEG](/sequence-files/IGVFFI7657MMEG/), [IGVFFI3122LZPJ](/sequence-files/IGVFFI3122LZPJ/), [IGVFFI5457XBYW](/sequence-files/IGVFFI5457XBYW/), [IGVFFI9145VWFH](/sequence-files/IGVFFI9145VWFH/), [IGVFFI8017PIDE](/sequence-files/IGVFFI8017PIDE/) 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/IGVFDS8995GXYE/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8995GXYE](/auxiliary-sets/IGVFDS8995GXYE/) 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/IGVFDS8995GXYE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8995GXYE/",
"accession": "IGVFDS8995GXYE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinA_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": "2023-12-01T00:05:31.485273+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": "2023-12-20T23:06:33.773212+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4125CFFV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4125CFFV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinA"
],
"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 0-25% 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": "2023-12-05T19:27:27.649099+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": "99ba73dd-46fa-4286-b8bf-52433d3427ba"
}