{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0965VVJT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0965VVJT",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-chronic-activation-batf3-rep1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0965VVJT](/measurement-sets/IGVFDS0965VVJT/) has sequence file(s) [IGVFFI1583LDHP](/sequence-files/IGVFFI1583LDHP/), [IGVFFI1611NVSI](/sequence-files/IGVFFI1611NVSI/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS0965VVJT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0965VVJT](/measurement-sets/IGVFDS0965VVJT/) has sequence file(s): [IGVFFI1583LDHP](/sequence-files/IGVFFI1583LDHP/), [IGVFFI1611NVSI](/sequence-files/IGVFFI1611NVSI/) 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": "/measurement-sets/IGVFDS0965VVJT/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8821YQXI](/primary-cells/IGVFSM8821YQXI/) 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/IGVFSM8821YQXI/"
}
]
},
"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_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4221ZTFC/",
"accession": "IGVFDS4221ZTFC",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-chronic-activation-gfp-rep1"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-08T19:37:42.998724+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9588OERW/",
"accession": "IGVFDO9588OERW",
"aliases": [
"charles-gersbach:cd8-tcells-donor-9"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1583LDHP/",
"accession": "IGVFFI1583LDHP",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-chronic-activation-batf3-rep1-fastq-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-08T21:15:25.947899+00:00",
"file_format": "fastq",
"file_size": 1489500771,
"href": "/sequence-files/IGVFFI1583LDHP/@@download/IGVFFI1583LDHP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/66a4a100-f56e-418d-aad8-8441d5190454/IGVFFI1583LDHP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"term_name": "Illumina NovaSeq 6000"
},
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM65-IL-2-D1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1611NVSI/",
"accession": "IGVFFI1611NVSI",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-chronic-activation-batf3-rep1-fastq-R2"
],
"content_type": "reads",
"creation_timestamp": "2023-11-08T21:16:17.517268+00:00",
"file_format": "fastq",
"file_size": 1544021429,
"href": "/sequence-files/IGVFFI1611NVSI/@@download/IGVFFI1611NVSI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/ad8e14d7-4d5e-469c-87b9-e298be9aeec1/IGVFFI1611NVSI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"term_name": "Illumina NovaSeq 6000"
},
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM65-IL-2-D1_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5066GYDY/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"notes": "This file_set previously had f9e9ffe1-b463-4b15-964c-e926bfcf58a8 submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
"preferred_assay_title": "RNA-seq",
"protocols": [
"https://www.protocols.io/view/rnaseq-of-primary-human-t-cells-overexpressing-bat-c5pdy5i6"
],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-10-29T17:38:48.256647+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM8821YQXI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8821YQXI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1868WXHB/",
"accession": "IGVFDS1868WXHB",
"file_set_type": "expression vector library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000123685/",
"geneid": "ENSG00000123685",
"name": "basic leucine zipper ATF-like transcription factor 3",
"summary": "BATF3 - ENSG00000123685 (Homo sapiens)",
"symbol": "BATF3"
}
],
"summary": "Expression vector library of BATF3"
}
],
"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 transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-08T21:15:25.947899+00:00",
"summary": "RNA-seq integrating a expression vector library of BATF3",
"uuid": "39de6306-b6b9-4cb2-a849-bb6ee1fde5ee"
}