{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5239SBBT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5239SBBT",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-perturb-seq-crispra"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8036VPRU](/primary-cells/IGVFSM8036VPRU/) 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/IGVFSM8036VPRU/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6223YCQV](/primary-cells/IGVFSM6223YCQV/) 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/IGVFSM6223YCQV/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2105CLXS](/primary-cells/IGVFSM2105CLXS/) 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/IGVFSM2105CLXS/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"control_for": [],
"creation_timestamp": "2024-10-01T15:11:10.725095+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4425KRAT/",
"accession": "IGVFDO4425KRAT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-8"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO6082RNLT/",
"accession": "IGVFDO6082RNLT",
"aliases": [
"charles-gersbach:cd8-tcells-donor-7"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7605NZFO/",
"accession": "IGVFDO7605NZFO",
"aliases": [
"charles-gersbach:cd8-tcells-donor-6"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI6830YLEK/",
"accession": "IGVFFI6830YLEK",
"aliases": [
"charles-gersbach:cd8-tcells-perturb-seq-10x-5prime-crispra-de-mast-results"
],
"assembly": "GRCh38",
"content_type": "differential gene expression quantifications",
"creation_timestamp": "2024-10-01T15:05:01.453142+00:00",
"file_format": "tsv",
"file_size": 23487211,
"href": "/tabular-files/IGVFFI6830YLEK/@@download/IGVFFI6830YLEK.tsv.gz",
"s3_uri": "s3://igvf-files/2024/10/01/cfabf8f2-5332-4452-a521-9dcf03b952fe/IGVFFI6830YLEK.tsv.gz",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/grna.de.crispra.umi_thres_4.aggr.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS4011VZXE/",
"accession": "IGVFDS4011VZXE",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-set-perturb-seq-crispra"
],
"file_set_type": "intermediate analysis"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-10-18T19:50:01.634631+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/primary-cells/IGVFSM8036VPRU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8036VPRU",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM6223YCQV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6223YCQV",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM2105CLXS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2105CLXS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0821YMMV/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-10-01T15:05:01.453142+00:00",
"summary": "activation Perturb-seq: differential gene expression quantifications",
"uuid": "a5f775f7-1681-4552-b045-6d06acb8a4ee",
"workflows": [
{
"@id": "/workflows/IGVFWF5701UESO/",
"accession": "IGVFWF5701UESO",
"name": "Gersbach Perturb-seq workflow"
}
]
}