{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2443IKFM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2443IKFM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE_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 [IGVFSM0787QFVT](/in-vitro-systems/IGVFSM0787QFVT/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0787QFVT/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2443IKFM](/measurement-sets/IGVFDS2443IKFM/) has in progress subobject auxiliary set [IGVFDS8247YIDV](/auxiliary-sets/IGVFDS8247YIDV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2443IKFM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8247YIDV](/auxiliary-sets/IGVFDS8247YIDV/) has sequence file(s) [IGVFFI8732THFQ](/sequence-files/IGVFFI8732THFQ/), [IGVFFI9078JOPW](/sequence-files/IGVFFI9078JOPW/), [IGVFFI6596UXNN](/sequence-files/IGVFFI6596UXNN/), [IGVFFI8402EJCS](/sequence-files/IGVFFI8402EJCS/), [IGVFFI7144JIEE](/sequence-files/IGVFFI7144JIEE/), [IGVFFI7474NWFW](/sequence-files/IGVFFI7474NWFW/), [IGVFFI7132RPVS](/sequence-files/IGVFFI7132RPVS/), [IGVFFI4395FBMH](/sequence-files/IGVFFI4395FBMH/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8247YIDV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8247YIDV](/auxiliary-sets/IGVFDS8247YIDV/) has sequence file(s): [IGVFFI8732THFQ](/sequence-files/IGVFFI8732THFQ/), [IGVFFI9078JOPW](/sequence-files/IGVFFI9078JOPW/), [IGVFFI6596UXNN](/sequence-files/IGVFFI6596UXNN/), [IGVFFI8402EJCS](/sequence-files/IGVFFI8402EJCS/), [IGVFFI7144JIEE](/sequence-files/IGVFFI7144JIEE/), [IGVFFI7474NWFW](/sequence-files/IGVFFI7474NWFW/), [IGVFFI7132RPVS](/sequence-files/IGVFFI7132RPVS/), [IGVFFI4395FBMH](/sequence-files/IGVFFI4395FBMH/) 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/IGVFDS8247YIDV/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2443IKFM](/measurement-sets/IGVFDS2443IKFM/) 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/IGVFDS2443IKFM/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8247YIDV](/auxiliary-sets/IGVFDS8247YIDV/) 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_for",
"path": "/auxiliary-sets/IGVFDS8247YIDV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8247YIDV/",
"accession": "IGVFDS8247YIDV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE_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/IGVFDS6385JXFZ/",
"accession": "IGVFDS6385JXFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:46:51.778478+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS5056OAGR/"
],
"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": "2023-12-20T23:09:27.503540+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0787QFVT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0787QFVT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-BinE"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"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 80-90% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:33:35.858194+00:00",
"summary": "prime editing 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": "c64d7c63-1e88-4b8f-abc2-e764dcb328da"
}