{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4213FGQT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4213FGQT",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-b2m-high-bin-rep1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2625BWKZ](/auxiliary-sets/IGVFDS2625BWKZ/) has sequence file(s): [IGVFFI7799MHFQ](/sequence-files/IGVFFI7799MHFQ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2625BWKZ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6062UNTJ](/primary-cells/IGVFSM6062UNTJ/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM6062UNTJ/"
},
{
"category": "missing files",
"detail": "Measurement set [IGVFDS4213FGQT](/measurement-sets/IGVFDS4213FGQT/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS4213FGQT/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4213FGQT](/measurement-sets/IGVFDS4213FGQT/) 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/IGVFDS4213FGQT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2625BWKZ/",
"accession": "IGVFDS2625BWKZ",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-high-bin-rep1"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5357XHOF/",
"accession": "IGVFDS5357XHOF",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-b2m-low-bin-rep1"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-08T19:32:33.337711+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8199EHWU/",
"accession": "IGVFDO8199EHWU",
"aliases": [
"charles-gersbach:cd8-tcells-donor-17"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This file_set previously had 5d15ca93-89fb-4a34-8863-001eda25bb4c submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
"preferred_assay_title": "CRISPR FACS screen",
"protocols": [
"https://www.protocols.io/view/car-t-cell-characterization-by-flow-cytometry-c48qyzvw",
"https://www.protocols.io/view/crispri-tiling-screens-c5rby52n"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
],
"status": "released"
}
],
"release_timestamp": "2024-11-19T20:35:12.998703+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM6062UNTJ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6062UNTJ",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-high-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5026WRUO/",
"accession": "IGVFDS5026WRUO",
"file_set_type": "guide library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000166710/",
"geneid": "ENSG00000166710",
"name": "beta-2-microglobulin",
"status": "released",
"summary": "B2M - ENSG00000166710 (Homo sapiens)",
"symbol": "B2M"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in B2M"
}
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens (sorting details: FACS bin for 90-100% expression of b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-08T20:28:15.533066+00:00",
"summary": "CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in B2M",
"targeted_genes": [
{
"@id": "/genes/ENSG00000166710/",
"geneid": "ENSG00000166710",
"name": "beta-2-microglobulin",
"status": "released",
"symbol": "B2M",
"synonyms": [
"beta chain of MHC class I molecules",
"beta-2-microglobulin",
"IMD43",
"beta-2-microglobin"
]
}
],
"uuid": "75b0479a-e64e-4df0-8208-3c634ad94a6f"
}