{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2606RJRX/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2606RJRX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2606RJRX](/auxiliary-sets/IGVFDS2606RJRX/) has sequence file(s): [IGVFFI7351KKAC](/sequence-files/IGVFFI7351KKAC/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2606RJRX/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3895SURE](/primary-cells/IGVFSM3895SURE/) 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/IGVFSM3895SURE/"
}
]
},
"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": "2024-02-05T22:39:41.681789+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8306NDTY/",
"accession": "IGVFDO8306NDTY",
"aliases": [
"charles-gersbach:cd8-tcells-donor-25"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7351KKAC/",
"accession": "IGVFFI7351KKAC",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep1-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-08T20:29:59.117201+00:00",
"file_format": "fastq",
"file_size": 549544531,
"href": "/sequence-files/IGVFFI7351KKAC/@@download/IGVFFI7351KKAC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/3e909f0e-bd99-41b1-ac2a-37495af831a9/IGVFFI7351KKAC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0004205/",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM74_L2_S8_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7944XZYE/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3910ZTSZ/",
"accession": "IGVFDS3910ZTSZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"preferred_assay_title": "CRISPR FACS screen"
}
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-11-18T21:09:01.600762+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM3895SURE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3895SURE",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS3667PLQB/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"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 (sorting details: FACS bin for 0-10% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-08T20:29:59.117201+00:00",
"summary": "gRNA sequencing for CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "5849bf55-5445-427e-82de-dcfd1509dd31"
}