{
"@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/",
"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 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": "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": "validation error: preferred_assay_titles/1",
"detail": "Assay term [OBI_0003661](/assay-terms/OBI_0003661/) has schema error 'Variant FlowFISH' is not one of ['RNA-seq', 'scRNA-seq', 'snRNA-seq', 'scNT-seq', 'scNT-seq2', 'Parse SPLiT-seq', 'ATAC-seq', 'scATAC-seq', 'snATAC-seq', 'DOGMA-seq', '10x multiome', '10x multiome with MULTI-seq', 'MULTI-seq', 'SHARE-seq', 'Histone ChIP-seq', 'TF ChIP-seq', 'MPRA', 'MPRA (scQer)', 'AAV-MPRA', 'lentiMPRA', 'STARR-seq', 'SUPERSTARR', 'Cell painting', 'Variant painting via fluorescence', 'Variant painting via immunostaining', 'smFISH', 'MERFISH', 'Proliferation CRISPR screen', 'Growth CRISPR screen', 'Migration CRISPR screen', 'CRISPR FlowFISH screen', 'CRISPR FACS screen', 'CRISPR mCherry screen', 'HCR-FlowFISH screen', 'scCRISPR screen', 'Perturb-seq', 'CERES-seq', 'TAP-seq', 'Variant-EFFECTS', 'SGE', 'MIAA', 'snmC-Seq2', 'snMCT-seq', 'snM3C-seq', 'mN2H', 'semi-qY2H', 'Y2H', 'yN2H', 'VAMP-seq', 'VAMP-seq (MultiSTEP)', 'Hi-C', 'HiCAR', 'Spatial transcriptomics', 'HT-recruit', 'ONT dRNA', 'ONT Fiber-seq', 'ONT direct WGS'].",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/assay-terms/OBI_0003661/"
},
{
"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 auxiliary set",
"detail": "Measurement set [IGVFDS5518TESD](/measurement-sets/IGVFDS5518TESD/) has no variant sequencing `auxiliary_sets`. Variant-EFFECTS measurement sets are expected to link to a variant sequencing auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5518TESD/"
},
{
"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": 50,
"level_name": "NOT_COMPLIANT",
"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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS5518TESD/"
}
],
"WARNING": [
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS5518TESD](/measurement-sets/IGVFDS5518TESD/) has `assay_term` in vitro CRISPR screen using flow cytometry, but `preferred_assay_title` Variant-EFFECTS. Measurement sets are expected to specify an appropriate preferred assay title for its respective assay term.",
"level": 40,
"level_name": "WARNING",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/IGVFDS5518TESD/"
}
]
},
"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/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"
]
}
],
"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"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7068CPID/",
"accession": "IGVFDS7068CPID",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/84486717-53c5-477a-bff0-e686dc38d8a7/",
"modality": "prime editing"
}
],
"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": "Jurkat cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/98fb23d3-0d79-4c3d-981d-01539e6589f1/",
"title": "Idan Gabdank"
},
"summary": "prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "fd86ed6d-e3d5-45d6-b8fb-ae5e113190b2"
}