{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5825GTXD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5825GTXD",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-ccr7-low-bin-rep2"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5825GTXD](/auxiliary-sets/IGVFDS5825GTXD/) has sequence file(s): [IGVFFI5991TZXM](/sequence-files/IGVFFI5991TZXM/) 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/IGVFDS5825GTXD/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM9398LTWW](/primary-cells/IGVFSM9398LTWW/) 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/IGVFSM9398LTWW/"
}
]
},
"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": "2024-02-05T22:39:29.595021+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO5479ZYLJ/",
"accession": "IGVFDO5479ZYLJ",
"aliases": [
"charles-gersbach:cd8-tcells-donor-21"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI5991TZXM/",
"accession": "IGVFFI5991TZXM",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-ccr7-low-bin-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:28:50.841680+00:00",
"file_format": "fastq",
"file_size": 13137180,
"href": "/sequence-files/IGVFFI5991TZXM/@@download/IGVFFI5991TZXM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/f9545164-4ca8-4ac6-9869-93c80141664c/IGVFFI5991TZXM.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/CCR7pos-pSM27-TF-L3_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9065THHI/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6902RBPO/",
"accession": "IGVFDS6902RBPO",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-ccr7-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": "2024-11-18T21:09:09.337987+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM9398LTWW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9398LTWW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-ccr7-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"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 CCR7) 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": "2023-11-08T20:28:50.841680+00:00",
"summary": "gRNA sequencing for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "94f94032-559f-4647-8c9e-1ea3f9eac598"
}