{
"@context": "/terms/",
"@id": "/primary-cells/IGVFSM2747RJFY/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747RJFY",
"age": "unknown",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-rep2"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS0821YMMV](/construct-library-sets/IGVFDS0821YMMV/) has revoked subobject tabular file [IGVFFI1405WMSH](/tabular-files/IGVFFI1405WMSH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS0821YMMV/"
},
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS0821YMMV](/construct-library-sets/IGVFDS0821YMMV/) has in progress subobject tabular file [IGVFFI2489BLJI](/tabular-files/IGVFFI2489BLJI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS0821YMMV/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2747RJFY](/primary-cells/IGVFSM2747RJFY/) 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/IGVFSM2747RJFY/"
},
{
"category": "missing files",
"detail": "Construct library set [IGVFDS0821YMMV](/construct-library-sets/IGVFDS0821YMMV/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS0821YMMV/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0821YMMV/",
"accession": "IGVFDS0821YMMV",
"file_set_type": "guide library",
"status": "released"
}
],
"creation_timestamp": "2023-11-08T19:28:23.350156+00:00",
"description": "Lentivirus encoding for CRISPRi (dSaCas9-KRAB) and a TF-targeting gRNA library",
"donors": [
"/human-donors/IGVFDO6082RNLT/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS1333MBPK/",
"accession": "IGVFDS1333MBPK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-gex-rep2"
],
"file_set_type": "experimental data",
"lab": {
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "Perturb-seq",
"status": "released",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes"
},
{
"@id": "/auxiliary-sets/IGVFDS2399UCGA/",
"accession": "IGVFDS2399UCGA",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-crispri-grna-rep2"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes"
},
{
"@id": "/curated-sets/IGVFDS4729GLXH/",
"accession": "IGVFDS4729GLXH",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-grnas-set"
],
"file_set_type": "guide RNAs",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "Homo sapiens GRCh38 guide RNAs"
},
{
"@id": "/analysis-sets/IGVFDS3319RFFN/",
"accession": "IGVFDS3319RFFN",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-set-perturb-seq-crispri"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "interference Perturb-seq: filtered feature barcode matrix"
},
{
"@id": "/analysis-sets/IGVFDS9445RJOU/",
"accession": "IGVFDS9445RJOU",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-perturb-seq-crispri"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Charles Gersbach, Duke"
},
"status": "released",
"summary": "interference Perturb-seq: differential gene expression 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": "2024-10-18T19:50:07.045252+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": [],
"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": "The ConstructLibrarySet on this Sample was upgraded from a ConstructLibrary attached to the FileSet it was connected to.",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens",
"uuid": "0abc3ccd-3b17-4ed9-97f4-b9daf8459d16",
"virtual": false
}