{
"@context": "/terms/",
"@id": "/primary-cells/IGVFSM3895SURE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3895SURE",
"age": "unknown",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS3667PLQB](/construct-library-sets/IGVFDS3667PLQB/) has in progress subobject reference file [IGVFFI6537JARB](/reference-files/IGVFFI6537JARB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS3667PLQB/"
},
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS3667PLQB](/construct-library-sets/IGVFDS3667PLQB/) has in progress subobject tabular file [IGVFFI9735DZKB](/tabular-files/IGVFFI9735DZKB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS3667PLQB/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3895SURE](/primary-cells/IGVFSM3895SURE/) 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/IGVFSM3895SURE/"
},
{
"category": "missing files",
"detail": "Construct library set [IGVFDS3667PLQB](/construct-library-sets/IGVFDS3667PLQB/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS3667PLQB/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS3667PLQB/",
"accession": "IGVFDS3667PLQB",
"file_set_type": "guide library"
}
],
"creation_timestamp": "2023-11-08T19:01:11.357208+00:00",
"donors": [
"/human-donors/IGVFDO8306NDTY/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS3910ZTSZ/",
"accession": "IGVFDS3910ZTSZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "CRISPR FACS screen",
"status": "released",
"summary": "CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes"
},
{
"@id": "/auxiliary-sets/IGVFDS2606RJRX/",
"accession": "IGVFDS2606RJRX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "gRNA sequencing for CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes"
},
{
"@id": "/curated-sets/IGVFDS8695PIUQ/",
"accession": "IGVFDS8695PIUQ",
"aliases": [
"charles-gersbach:tfome-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/IGVFDS7944XZYE/",
"accession": "IGVFDS7944XZYE",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispr-ko-tfome-batf3-over"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "CRISPR knockout FACS screen targeting IL7R: alignments"
},
{
"@id": "/analysis-sets/IGVFDS8364HJHL/",
"accession": "IGVFDS8364HJHL",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-crispr-ko-tfome-batf3-over"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "CRISPR knockout FACS screen targeting IL7R: fold change over control, guide quantifications"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"cas": "Cas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"modality": "knockout",
"status": "released",
"summary": "CRISPRko Sp-Cas9"
}
],
"moi": 0.4,
"multiplexed_in": [],
"notes": "This sample's modifications originally included Modification /modifications/293e629b-5d15-49d7-aacb-19be40d9da03/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_293e629b-5d15-49d7-aacb-19be40d9da03.",
"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"
]
}
],
"release_timestamp": "2024-11-18T21:09:01.625675+00:00",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"schema_version": "21",
"sex": "unspecified",
"sorted_fractions": [],
"sorted_from": {
"@id": "/primary-cells/IGVFSM2824DRGN/",
"accession": "IGVFSM2824DRGN"
},
"sorted_from_detail": "FACS bin for 0-10% expression of IL7R in cells overexpressing BATF3",
"sources": [
{
"@id": "/sources/stem-cell-technologies/",
"title": "STEMCELL Technologies"
}
],
"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 IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens",
"uuid": "93e45b18-f247-4061-8e7e-15238cbccefc",
"virtual": false
}