{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1345STXL/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1345STXL",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-low-bin-rep1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1345STXL](/auxiliary-sets/IGVFDS1345STXL/) has sequence file(s): [IGVFFI2002GGIA](/sequence-files/IGVFFI2002GGIA/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS1345STXL/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4936HKEW](/primary-cells/IGVFSM4936HKEW/) 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/IGVFSM4936HKEW/"
}
]
},
"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": "2024-02-05T22:39:30.518269+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4646JDEN/",
"accession": "IGVFDO4646JDEN",
"aliases": [
"charles-gersbach:cd8-tcells-donor-23"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI2002GGIA/",
"accession": "IGVFFI2002GGIA",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-low-bin-rep1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:28:59.077623+00:00",
"file_format": "fastq",
"file_size": 800205032,
"href": "/sequence-files/IGVFFI2002GGIA/@@download/IGVFFI2002GGIA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/dbf16ef8-b176-4a14-b4dc-561a1ac0e682/IGVFFI2002GGIA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0004205/",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM73_L2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5551EATG/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5130AKAZ/",
"accession": "IGVFDS5130AKAZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-low-bin-rep1"
],
"preferred_assay_title": "CRISPR FACS screen",
"status": "released"
}
],
"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": "2024-11-18T21:09:11.082295+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM4936HKEW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4936HKEW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS3667PLQB/"
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"status": "released"
}
],
"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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-08T20:28:59.077623+00:00",
"summary": "gRNA sequencing for CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "7c686d53-23d9-49fd-9537-7c31be817c7c"
}