{
"@context": "/terms/",
"@id": "/primary-cells/IGVFSM7117ATUZ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7117ATUZ",
"age": "unknown",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-gata3-rep3"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS2398ZXBQ](/construct-library-sets/IGVFDS2398ZXBQ/) has in progress subobject tabular file [IGVFFI5895HWMM](/tabular-files/IGVFFI5895HWMM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS2398ZXBQ/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS2398ZXBQ](/construct-library-sets/IGVFDS2398ZXBQ/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS2398ZXBQ/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7117ATUZ](/primary-cells/IGVFSM7117ATUZ/) 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/IGVFSM7117ATUZ/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2398ZXBQ/",
"accession": "IGVFDS2398ZXBQ",
"file_set_type": "guide library"
}
],
"creation_timestamp": "2023-11-08T19:00:03.756555+00:00",
"description": "Lentivirus encoding for GATA3 targeting gRNA",
"donors": [
"/human-donors/IGVFDO4048LCOU/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS3969UCCQ/",
"accession": "IGVFDS3969UCCQ",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep3"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "RNA-seq",
"status": "released",
"summary": "knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3"
},
{
"@id": "/curated-sets/IGVFDS0876APCC/",
"accession": "IGVFDS0876APCC",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-gata3-grnas-set"
],
"file_set_type": "guide RNAs",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "in progress",
"summary": "Homo sapiens GRCh38 guide RNAs"
},
{
"@id": "/analysis-sets/IGVFDS0006MFFD/",
"accession": "IGVFDS0006MFFD",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-cas-ko-gata3"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "knockout RNA-seq: transcriptome alignments"
},
{
"@id": "/analysis-sets/IGVFDS7239LNZO/",
"accession": "IGVFDS7239LNZO",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-cas-ko-gata3"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "knockout 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"
},
"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": "2024-10-25T04:18:36.439585+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 activated with CD3/CD28 dynabeads at a 1:1 ratio. At 24 hours post-activation, CD8+ T cells were transduced with gRNA lentivirus encoding a GATA3 targeting gRNA. At 48 hours post-activation, 3.5 x 10^5 T cells were electroporated with Cas9 protein. Briefly, cells were collected, spun down at 90xg for 10 minutes, resuspended in 20uL of Lonza P3 Primary buffer with 1.12 ug Cas9, and electroporated with the pulse code EH115. 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).\n\nT cells were maintained at a concentration of 1-2e6 per mL for 9 days before RNA-sequencing.\nRNA was harvested using Norgen's Total RNA Purification Kit.\nRNA libraries for RNA-seq were prepared by Azenta Life Sciences.",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens",
"uuid": "07d0b739-16f3-49c7-a891-c1bfb8633289",
"virtual": false
}