{
"@context": "/terms/",
"@id": "/primary-cells/IGVFSM0383IKGE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0383IKGE",
"age": "unknown",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-nt-rep3"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Construct library set [IGVFDS9830PJVQ](/construct-library-sets/IGVFDS9830PJVQ/) has no `control_for`. The `control_file_sets` should be patched on the file sets it serves as a control for and this property, `control_for`, will be reverse calculated. File sets that specify a control type are expected to be a control for other file sets.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_control_for_control_type",
"path": "/construct-library-sets/IGVFDS9830PJVQ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0383IKGE](/primary-cells/IGVFSM0383IKGE/) 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/IGVFSM0383IKGE/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9830PJVQ/",
"accession": "IGVFDS9830PJVQ",
"file_set_type": "guide library",
"status": "released"
}
],
"creation_timestamp": "2023-11-08T18:59:56.348916+00:00",
"description": "Lentivirus encoding for the nontargeting gRNA",
"donors": [
{
"@id": "/human-donors/IGVFDO4048LCOU/",
"accession": "IGVFDO4048LCOU",
"status": "released"
}
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS9846EQXV/",
"accession": "IGVFDS9846EQXV",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-nt-rep3"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "RNA-seq",
"status": "released",
"summary": "non-targeting CRISPR knockout RNA-seq integrating a non-targeting guide (sgRNA) library"
},
{
"@id": "/curated-sets/IGVFDS1053LAWX/",
"accession": "IGVFDS1053LAWX",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-nt-grnas-set"
],
"file_set_type": "guide RNAs",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "in progress",
"summary": "Homo sapiens GRCh38 guide RNAs"
},
{
"@id": "/analysis-sets/IGVFDS6924DJJC/",
"accession": "IGVFDS6924DJJC",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-rna-seq-cas-ko-nt"
],
"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, transcriptome alignments"
},
{
"@id": "/analysis-sets/IGVFDS9906UGWB/",
"accession": "IGVFDS9906UGWB",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-rna-seq-cas-ko-znf217"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "knockout RNA-seq: fold change over control, transcript quantifications, transcriptome alignments"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
"certificate_identifier": "IP117-01",
"controlled_access": false,
"status": "released"
}
],
"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"
],
"status": "released"
}
],
"release_timestamp": "2024-10-25T04:18:36.068222+00:00",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"schema_version": "22",
"sex": "unspecified",
"sorted_fractions": [],
"sources": [
{
"@id": "/sources/stem-cell-technologies/",
"status": "released",
"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 non-targeting (NT) 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": "Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens",
"uuid": "936d2d41-6956-43a2-b031-3ebc973d0837",
"virtual": false
}