{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7952EIJE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7952EIJE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-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 in vitro system [IGVFSM7227LRMC](/in-vitro-systems/IGVFSM7227LRMC/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM7227LRMC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7952EIJE](/measurement-sets/IGVFDS7952EIJE/) has in progress subobject auxiliary set [IGVFDS4055OGPS](/auxiliary-sets/IGVFDS4055OGPS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7952EIJE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4055OGPS](/auxiliary-sets/IGVFDS4055OGPS/) has sequence file(s): [IGVFFI1564SMJH](/sequence-files/IGVFFI1564SMJH/), [IGVFFI0076OEIC](/sequence-files/IGVFFI0076OEIC/), [IGVFFI0145MUWW](/sequence-files/IGVFFI0145MUWW/), [IGVFFI2948EAHB](/sequence-files/IGVFFI2948EAHB/), [IGVFFI4402LLVP](/sequence-files/IGVFFI4402LLVP/), [IGVFFI6757WSBK](/sequence-files/IGVFFI6757WSBK/), [IGVFFI6517NKMR](/sequence-files/IGVFFI6517NKMR/), [IGVFFI7908RYZM](/sequence-files/IGVFFI7908RYZM/), [IGVFFI0714JYYV](/sequence-files/IGVFFI0714JYYV/), [IGVFFI6113UAKW](/sequence-files/IGVFFI6113UAKW/), [IGVFFI3590MOHL](/sequence-files/IGVFFI3590MOHL/), [IGVFFI8515ACGC](/sequence-files/IGVFFI8515ACGC/), [IGVFFI6173LYCI](/sequence-files/IGVFFI6173LYCI/), [IGVFFI3130RSFU](/sequence-files/IGVFFI3130RSFU/), [IGVFFI6198EEDN](/sequence-files/IGVFFI6198EEDN/), [IGVFFI9067FCQX](/sequence-files/IGVFFI9067FCQX/), [IGVFFI0300SRFQ](/sequence-files/IGVFFI0300SRFQ/), [IGVFFI9787EIJU](/sequence-files/IGVFFI9787EIJU/), [IGVFFI9296ENTV](/sequence-files/IGVFFI9296ENTV/), [IGVFFI7080RWUC](/sequence-files/IGVFFI7080RWUC/), [IGVFFI6583PLEK](/sequence-files/IGVFFI6583PLEK/), [IGVFFI2313GOLM](/sequence-files/IGVFFI2313GOLM/), [IGVFFI5536WZYG](/sequence-files/IGVFFI5536WZYG/), [IGVFFI0710HGEY](/sequence-files/IGVFFI0710HGEY/), [IGVFFI1089YVZH](/sequence-files/IGVFFI1089YVZH/), [IGVFFI1987LCLC](/sequence-files/IGVFFI1987LCLC/), [IGVFFI6787NHPX](/sequence-files/IGVFFI6787NHPX/), [IGVFFI6665FFDW](/sequence-files/IGVFFI6665FFDW/), [IGVFFI5957NNRJ](/sequence-files/IGVFFI5957NNRJ/), [IGVFFI5022ULFN](/sequence-files/IGVFFI5022ULFN/), [IGVFFI0783XXZF](/sequence-files/IGVFFI0783XXZF/), [IGVFFI0591CWVC](/sequence-files/IGVFFI0591CWVC/), [IGVFFI0261FAMQ](/sequence-files/IGVFFI0261FAMQ/), [IGVFFI4632VTSL](/sequence-files/IGVFFI4632VTSL/), [IGVFFI6840ABLE](/sequence-files/IGVFFI6840ABLE/), [IGVFFI3067KPLY](/sequence-files/IGVFFI3067KPLY/), [IGVFFI4260LLZL](/sequence-files/IGVFFI4260LLZL/), [IGVFFI3621IAGP](/sequence-files/IGVFFI3621IAGP/), [IGVFFI1136RWNM](/sequence-files/IGVFFI1136RWNM/), [IGVFFI0411WPYA](/sequence-files/IGVFFI0411WPYA/), [IGVFFI7199JLFV](/sequence-files/IGVFFI7199JLFV/), [IGVFFI8059CXAW](/sequence-files/IGVFFI8059CXAW/), [IGVFFI2471VZYB](/sequence-files/IGVFFI2471VZYB/), [IGVFFI3063ZZYV](/sequence-files/IGVFFI3063ZZYV/), [IGVFFI0671ZFVC](/sequence-files/IGVFFI0671ZFVC/), [IGVFFI9812FANR](/sequence-files/IGVFFI9812FANR/), [IGVFFI0897ZSVE](/sequence-files/IGVFFI0897ZSVE/), [IGVFFI1999LQNJ](/sequence-files/IGVFFI1999LQNJ/) 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/IGVFDS4055OGPS/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7952EIJE](/measurement-sets/IGVFDS7952EIJE/) 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/IGVFDS7952EIJE/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4055OGPS](/auxiliary-sets/IGVFDS4055OGPS/) has sequence file(s) [IGVFFI1564SMJH](/sequence-files/IGVFFI1564SMJH/), [IGVFFI0076OEIC](/sequence-files/IGVFFI0076OEIC/), [IGVFFI0145MUWW](/sequence-files/IGVFFI0145MUWW/), [IGVFFI2948EAHB](/sequence-files/IGVFFI2948EAHB/), [IGVFFI4402LLVP](/sequence-files/IGVFFI4402LLVP/), [IGVFFI6757WSBK](/sequence-files/IGVFFI6757WSBK/), [IGVFFI6517NKMR](/sequence-files/IGVFFI6517NKMR/), [IGVFFI7908RYZM](/sequence-files/IGVFFI7908RYZM/), [IGVFFI0714JYYV](/sequence-files/IGVFFI0714JYYV/), [IGVFFI6113UAKW](/sequence-files/IGVFFI6113UAKW/), [IGVFFI3590MOHL](/sequence-files/IGVFFI3590MOHL/), [IGVFFI8515ACGC](/sequence-files/IGVFFI8515ACGC/), [IGVFFI6173LYCI](/sequence-files/IGVFFI6173LYCI/), [IGVFFI3130RSFU](/sequence-files/IGVFFI3130RSFU/), [IGVFFI6198EEDN](/sequence-files/IGVFFI6198EEDN/), [IGVFFI9067FCQX](/sequence-files/IGVFFI9067FCQX/), [IGVFFI0300SRFQ](/sequence-files/IGVFFI0300SRFQ/), [IGVFFI9787EIJU](/sequence-files/IGVFFI9787EIJU/), [IGVFFI9296ENTV](/sequence-files/IGVFFI9296ENTV/), [IGVFFI7080RWUC](/sequence-files/IGVFFI7080RWUC/), [IGVFFI6583PLEK](/sequence-files/IGVFFI6583PLEK/), [IGVFFI2313GOLM](/sequence-files/IGVFFI2313GOLM/), [IGVFFI5536WZYG](/sequence-files/IGVFFI5536WZYG/), [IGVFFI0710HGEY](/sequence-files/IGVFFI0710HGEY/), [IGVFFI1089YVZH](/sequence-files/IGVFFI1089YVZH/), [IGVFFI1987LCLC](/sequence-files/IGVFFI1987LCLC/), [IGVFFI6787NHPX](/sequence-files/IGVFFI6787NHPX/), [IGVFFI6665FFDW](/sequence-files/IGVFFI6665FFDW/), [IGVFFI5957NNRJ](/sequence-files/IGVFFI5957NNRJ/), [IGVFFI5022ULFN](/sequence-files/IGVFFI5022ULFN/), [IGVFFI0783XXZF](/sequence-files/IGVFFI0783XXZF/), [IGVFFI0591CWVC](/sequence-files/IGVFFI0591CWVC/), [IGVFFI0261FAMQ](/sequence-files/IGVFFI0261FAMQ/), [IGVFFI4632VTSL](/sequence-files/IGVFFI4632VTSL/), [IGVFFI6840ABLE](/sequence-files/IGVFFI6840ABLE/), [IGVFFI3067KPLY](/sequence-files/IGVFFI3067KPLY/), [IGVFFI4260LLZL](/sequence-files/IGVFFI4260LLZL/), [IGVFFI3621IAGP](/sequence-files/IGVFFI3621IAGP/), [IGVFFI1136RWNM](/sequence-files/IGVFFI1136RWNM/), [IGVFFI0411WPYA](/sequence-files/IGVFFI0411WPYA/), [IGVFFI7199JLFV](/sequence-files/IGVFFI7199JLFV/), [IGVFFI8059CXAW](/sequence-files/IGVFFI8059CXAW/), [IGVFFI2471VZYB](/sequence-files/IGVFFI2471VZYB/), [IGVFFI3063ZZYV](/sequence-files/IGVFFI3063ZZYV/), [IGVFFI0671ZFVC](/sequence-files/IGVFFI0671ZFVC/), [IGVFFI9812FANR](/sequence-files/IGVFFI9812FANR/), [IGVFFI0897ZSVE](/sequence-files/IGVFFI0897ZSVE/), [IGVFFI1999LQNJ](/sequence-files/IGVFFI1999LQNJ/) 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/IGVFDS4055OGPS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4055OGPS](/auxiliary-sets/IGVFDS4055OGPS/) 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/IGVFDS4055OGPS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4055OGPS/",
"accession": "IGVFDS4055OGPS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:04:43.426330+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/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:06:58.910929+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7227LRMC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7227LRMC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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": "2023-12-05T19:18:11.674627+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": "911aaffb-7a16-442f-ac4a-f3ab48d37aa0"
}