{
"@context": "/terms/",
"@id": "/primary-cells/IGVFSM8821YQXI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8821YQXI",
"age": "unknown",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep1"
],
"audit": {
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS1868WXHB](/construct-library-sets/IGVFDS1868WXHB/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS1868WXHB/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8821YQXI](/primary-cells/IGVFSM8821YQXI/) 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/IGVFSM8821YQXI/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1868WXHB/",
"accession": "IGVFDS1868WXHB",
"file_set_type": "expression vector library"
}
],
"creation_timestamp": "2023-11-08T19:00:35.070432+00:00",
"description": "Lentivirus encoding for HER2-CAR-2A-GFP or HER2-CAR-2A-BATF3",
"donors": [
"/human-donors/IGVFDO9588OERW/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS0986HRDF/",
"accession": "IGVFDS0986HRDF",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-rep1"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "ATAC-seq",
"status": "released",
"summary": "ATAC-seq integrating a expression vector library of BATF3"
},
{
"@id": "/measurement-sets/IGVFDS0965VVJT/",
"accession": "IGVFDS0965VVJT",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-chronic-activation-batf3-rep1"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "RNA-seq",
"status": "released",
"summary": "RNA-seq integrating a expression vector library of BATF3"
},
{
"@id": "/analysis-sets/IGVFDS9202ZPBI/",
"accession": "IGVFDS9202ZPBI",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-set-atac-seq-chronic-activation-batf3"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "ATAC-seq: alignments"
},
{
"@id": "/analysis-sets/IGVFDS5066GYDY/",
"accession": "IGVFDS5066GYDY",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-batf3-overexpression-batf3"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "RNA-seq: transcriptome alignments"
},
{
"@id": "/analysis-sets/IGVFDS6344XBAV/",
"accession": "IGVFDS6344XBAV",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-atac-seq-chronic-activation-batf3"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "ATAC-seq: fold change over control, peak quantifications"
},
{
"@id": "/analysis-sets/IGVFDS4582MPNU/",
"accession": "IGVFDS4582MPNU",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-batf3-overexpression"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "RNA-seq: fold change over control, transcript quantifications"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01"
}
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"multiplexed_in": [],
"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": "2024-10-29T17:33:31.610956+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": [],
"sources": [
{
"@id": "/sources/stem-cell-technologies/",
"title": "STEMCELL Technologies"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitter_comment": "CD8 T cells were cultured in PRIME-XV T cell expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed), 100 units/mL of penicilllin, 100 units/mL of streptomycin, and 100 units/mL human IL-2 (Peprotech).\nHuman CD8+ T cells were transduced with lentivirus encoding for either HER2-CAR-2A-GFP or HER2-CAR-2A-BATF3.\nT cells were stimulated repeatedly every three days with a 3:1 CD3/CD28 dynabead to cell ratio (chronic stimulation). \n50,000 transduced CD8 T cells were sorted for ATAC-seq on day 14.\nATAC-seq libraries were prepared according to the Omni ATAC-seq protocol.",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"uuid": "ddcbb03b-fa8e-4e2b-8d69-de386e5dbe62",
"virtual": false
}