{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9310VIMF/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9310VIMF",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-high-bin-rep3"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9310VIMF](/auxiliary-sets/IGVFDS9310VIMF/) has sequence file(s): [IGVFFI7647ERJF](/sequence-files/IGVFFI7647ERJF/) 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/IGVFDS9310VIMF/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1721KPGX](/primary-cells/IGVFSM1721KPGX/) 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/IGVFSM1721KPGX/"
}
]
},
"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": "2024-02-05T22:40:19.567054+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4579FYIL/",
"accession": "IGVFDO4579FYIL",
"aliases": [
"charles-gersbach:cd8-tcells-donor-22"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7647ERJF/",
"accession": "IGVFFI7647ERJF",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep3-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-08T20:33:58.631828+00:00",
"file_format": "fastq",
"file_size": 29319837,
"href": "/sequence-files/IGVFFI7647ERJF/@@download/IGVFFI7647ERJF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/fcf4b8b8-5a7e-4ff1-b57a-77409dc4d3d6/IGVFFI7647ERJF.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/CCR7pos-pSM54-TF-H3_S10_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4488GLKL/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5417LSWU/",
"accession": "IGVFDS5417LSWU",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep3"
],
"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": "2024-11-18T21:08:52.647018+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM1721KPGX/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1721KPGX",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"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 (sorting details: FACS bin for 90-100% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, 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": "2023-11-08T20:33:58.631828+00:00",
"summary": "gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "df1697ad-a720-4eb5-ad59-4cf5449fb0a5"
}