{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6878SUMX/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6878SUMX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-low-bin-rep3"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6878SUMX](/auxiliary-sets/IGVFDS6878SUMX/) has sequence file(s): [IGVFFI4454GSFQ](/sequence-files/IGVFFI4454GSFQ/) 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/IGVFDS6878SUMX/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4110AXZO](/primary-cells/IGVFSM4110AXZO/) 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/IGVFSM4110AXZO/"
}
]
},
"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": "2024-02-05T22:39:53.966669+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/IGVFFI4454GSFQ/",
"accession": "IGVFFI4454GSFQ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep3-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-08T20:31:07.525228+00:00",
"file_format": "fastq",
"file_size": 53566286,
"href": "/sequence-files/IGVFFI4454GSFQ/@@download/IGVFFI4454GSFQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/3d68199e-0eb1-460a-b931-b7b28d594b76/IGVFFI4454GSFQ.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-L3_S9_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/IGVFDS6262JHMS/",
"accession": "IGVFDS6262JHMS",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-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": "2024-11-18T21:08:52.708010+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM4110AXZO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4110AXZO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-low-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 0-10% 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": "2023-11-08T20:31:07.525228+00:00",
"summary": "gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"uuid": "ea2be8b1-36a1-48c5-a97e-1c88f2dbab74"
}