{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5627DEFZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5627DEFZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-low-bin-rep2"
],
"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 [IGVFDS0506WOIW](/auxiliary-sets/IGVFDS0506WOIW/) has sequence file(s): [IGVFFI3912VPFQ](/sequence-files/IGVFFI3912VPFQ/) 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/IGVFDS0506WOIW/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Measurement set [IGVFDS5627DEFZ](/measurement-sets/IGVFDS5627DEFZ/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS5627DEFZ/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5627DEFZ](/measurement-sets/IGVFDS5627DEFZ/) 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/IGVFDS5627DEFZ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4694MBIW](/primary-cells/IGVFSM4694MBIW/) 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/IGVFSM4694MBIW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0506WOIW/",
"accession": "IGVFDS0506WOIW",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-low-bin-rep2"
],
"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_for": [
{
"@id": "/measurement-sets/IGVFDS7661MIEF/",
"accession": "IGVFDS7661MIEF",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-high-bin-rep2"
],
"status": "released"
}
],
"creation_timestamp": "2023-11-08T19:32:26.049307+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4080HFHD/",
"accession": "IGVFDO4080HFHD",
"aliases": [
"charles-gersbach:cd8-tcells-donor-15"
],
"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": "2024-11-19T20:34:55.593705+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM4694MBIW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4694MBIW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS8345ZMZW/",
"accession": "IGVFDS8345ZMZW",
"file_set_type": "guide library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000116824/",
"geneid": "ENSG00000116824",
"name": "CD2 molecule",
"status": "released",
"summary": "CD2 - ENSG00000116824 (Homo sapiens)",
"symbol": "CD2"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in CD2"
}
],
"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 0-10% expression of CD2 ) 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": "2023-11-08T20:27:04.494082+00:00",
"summary": "CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in CD2",
"targeted_genes": [
{
"@id": "/genes/ENSG00000116824/",
"geneid": "ENSG00000116824",
"name": "CD2 molecule",
"status": "released",
"symbol": "CD2",
"synonyms": [
"SRBC",
"LFA-3 receptor",
"T11",
"rosette receptor",
"erythrocyte receptor",
"LFA-2",
"CD2 antigen (p50), sheep red blood cell receptor",
"T-cell surface antigen T11/Leu-5",
"lymphocyte-function antigen-2",
"T-cell surface antigen CD2"
]
}
],
"uuid": "98ac5484-b4f1-47db-8279-e3e9fe8dbd78"
}