{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5518TESD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5518TESD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing_idan"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5518TESD](/measurement-sets/IGVFDS5518TESD/) has deleted subobject measurement set [IGVFDS2892HZSS](/measurement-sets/IGVFDS2892HZSS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5518TESD/"
},
{
"category": "mismatched status",
"detail": "Archived in vitro system [IGVFSM6858FUVX](/in-vitro-systems/IGVFSM6858FUVX/) has in progress subobject source [atcc](/sources/atcc/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6858FUVX/"
},
{
"category": "mismatched status",
"detail": "Archived in vitro system [IGVFSM6858FUVX](/in-vitro-systems/IGVFSM6858FUVX/) has in progress subobject sample term [EFO_0002796](/sample-terms/EFO_0002796/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6858FUVX/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO1080XFGV](/human-donors/IGVFDO1080XFGV/) has in progress subobject phenotypic feature [0cc88904-d9f3-4ca2-8812-8557aa6445b4](/phenotypic-features/0cc88904-d9f3-4ca2-8812-8557aa6445b4/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO1080XFGV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Measurement set [IGVFDS5518TESD](/measurement-sets/IGVFDS5518TESD/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS5518TESD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5518TESD](/measurement-sets/IGVFDS5518TESD/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5518TESD/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5518TESD](/measurement-sets/IGVFDS5518TESD/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS5518TESD/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM6858FUVX](/in-vitro-systems/IGVFSM6858FUVX/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM6858FUVX/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7068CPID/",
"accession": "IGVFDS7068CPID",
"file_set_type": "guide library",
"status": "released",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS2892HZSS/",
"accession": "IGVFDS2892HZSS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "deleted"
}
],
"control_for": [],
"creation_timestamp": "2024-03-29T02:31:43.242619+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS7216VESH/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 553aa83a-922a-4663-9e05-1eb2b1e90434 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2024-03-22T23:04:37.145369+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6858FUVX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6858FUVX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_idan"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/84486717-53c5-477a-bff0-e686dc38d8a7/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "in progress",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "archived",
"summary": "Homo sapiens (male) Jurkat cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/98fb23d3-0d79-4c3d-981d-01539e6589f1/",
"title": "Idan Gabdank"
},
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "fd86ed6d-e3d5-45d6-b8fb-ae5e113190b2"
}