{
"@context": "/terms/",
"@id": "/primary-cells/IGVFSM3427LEEW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3427LEEW",
"age": "unknown",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-low-bin-rep2"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS5026WRUO](/construct-library-sets/IGVFDS5026WRUO/) has in progress subobject tabular file [IGVFFI1466VTFO](/tabular-files/IGVFFI1466VTFO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS5026WRUO/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS5026WRUO](/construct-library-sets/IGVFDS5026WRUO/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS5026WRUO/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3427LEEW](/primary-cells/IGVFSM3427LEEW/) 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/IGVFSM3427LEEW/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5026WRUO/",
"accession": "IGVFDS5026WRUO",
"file_set_type": "guide library",
"status": "released"
}
],
"creation_timestamp": "2023-11-08T19:00:49.545544+00:00",
"donors": [
"/human-donors/IGVFDO4200TDAP/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS3559YNWI/",
"accession": "IGVFDS3559YNWI",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-b2m-low-bin-rep2"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "CRISPR FACS screen",
"status": "released",
"summary": "CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in B2M"
},
{
"@id": "/auxiliary-sets/IGVFDS6947GSPF/",
"accession": "IGVFDS6947GSPF",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-low-bin-rep2"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "gRNA sequencing for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in B2M"
},
{
"@id": "/curated-sets/IGVFDS3778BYII/",
"accession": "IGVFDS3778BYII",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-b2m-grnas-set"
],
"file_set_type": "guide RNAs",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "in progress",
"summary": "Homo sapiens GRCh38 custom guide RNAs"
},
{
"@id": "/analysis-sets/IGVFDS2716FVEL/",
"accession": "IGVFDS2716FVEL",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispri-b2m"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "CRISPR interference FACS screen targeting B2M: alignments"
},
{
"@id": "/analysis-sets/IGVFDS8839AFQB/",
"accession": "IGVFDS8839AFQB",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-crispri-b2m"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "CRISPR interference FACS screen targeting B2M: fold change over control, guide quantifications"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"cas": "dCas9",
"cas_species": "Staphylococcus aureus (Sa)",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sa-dCas9"
}
],
"moi": 0.4,
"multiplexed_in": [],
"notes": "This sample's modifications originally included Modification /modifications/5d269861-f341-4629-a436-492fb432e132/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_5d269861-f341-4629-a436-492fb432e132.",
"nucleic_acid_delivery": "lentiviral transduction",
"origin_of": [],
"parts": [],
"pooled_in": [],
"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": "2024-11-18T21:09:14.526613+00:00",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"schema_version": "21",
"sex": "unspecified",
"sorted_fractions": [],
"sorted_from": {
"@id": "/primary-cells/IGVFSM0015KLZS/",
"accession": "IGVFSM0015KLZS",
"status": "released"
},
"sorted_from_detail": "FACS bin for 0-10% expression of b2m",
"sources": [
{
"@id": "/sources/zen-bioscience/",
"status": "released",
"title": "Zen Bioscience"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens (sorting details: FACS bin for 0-10% expression of b2m) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens",
"uuid": "29c9be4e-d6d9-4337-abfc-218e46d9dd1d",
"virtual": false
}