{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6947GSPF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6947GSPF",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-b2m-low-bin-rep2"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6947GSPF](/auxiliary-sets/IGVFDS6947GSPF/) has sequence file(s): [IGVFFI1999WHVY](/sequence-files/IGVFFI1999WHVY/) 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/IGVFDS6947GSPF/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3427LEEW](/primary-cells/IGVFSM3427LEEW/) 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/IGVFSM3427LEEW/"
}
]
},
"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": "2024-02-05T22:39:18.576580+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4200TDAP/",
"accession": "IGVFDO4200TDAP",
"aliases": [
"charles-gersbach:cd8-tcells-donor-18"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI1999WHVY/",
"accession": "IGVFFI1999WHVY",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-b2m-low-bin-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:27:40.744967+00:00",
"file_format": "fastq",
"file_size": 7072349,
"href": "/sequence-files/IGVFFI1999WHVY/@@download/IGVFFI1999WHVY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/9d18f996-d6e7-4e35-8c5f-89730ae0a361/IGVFFI1999WHVY.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/B2M-Low-R2_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2716FVEL/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3559YNWI/",
"accession": "IGVFDS3559YNWI",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-b2m-low-bin-rep2"
],
"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": "2024-11-18T21:09:14.480929+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM3427LEEW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3427LEEW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-b2m-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS5026WRUO/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"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 b2m) modified with CRISPRi Sa-dCas9, 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": "2023-11-08T20:27:40.744967+00:00",
"summary": "gRNA sequencing for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in B2M",
"uuid": "b5e9c274-d67c-4bb0-83f8-6cb12d1820f8"
}