{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0416TFEL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0416TFEL",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0416TFEL](/measurement-sets/IGVFDS0416TFEL/) has sequence file(s) [IGVFFI8155ZSDX](/sequence-files/IGVFFI8155ZSDX/), [IGVFFI4720GEPB](/sequence-files/IGVFFI4720GEPB/) 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/IGVFDS0416TFEL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0416TFEL](/measurement-sets/IGVFDS0416TFEL/) has sequence file(s): [IGVFFI8155ZSDX](/sequence-files/IGVFFI8155ZSDX/), [IGVFFI4720GEPB](/sequence-files/IGVFFI4720GEPB/) 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/IGVFDS0416TFEL/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0829UPAR](/primary-cells/IGVFSM0829UPAR/) 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/IGVFSM0829UPAR/"
}
]
},
"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": "2023-11-08T19:37:58.512628+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7589UJKG/",
"accession": "IGVFDO7589UJKG",
"aliases": [
"charles-gersbach:cd8-tcells-donor-13"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8155ZSDX/",
"accession": "IGVFFI8155ZSDX",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep2-fastq-R2"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:25:26.851257+00:00",
"file_format": "fastq",
"file_size": 2438816138,
"href": "/sequence-files/IGVFFI8155ZSDX/@@download/IGVFFI8155ZSDX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/a159c50a-302a-47a6-8ef9-16df67628ba4/IGVFFI8155ZSDX.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/pSM73-GATA3-2_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4720GEPB/",
"accession": "IGVFFI4720GEPB",
"aliases": [
"charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep2-fastq-R1"
],
"content_type": "reads",
"creation_timestamp": "2023-11-09T19:25:02.113892+00:00",
"file_format": "fastq",
"file_size": 2295962147,
"href": "/sequence-files/IGVFFI4720GEPB/@@download/IGVFFI4720GEPB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/09/89cb86b6-4c78-4219-8f10-325fe4b9b90a/IGVFFI4720GEPB.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/pSM73-GATA3-2_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0006MFFD/"
],
"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/tfome-crisprko-screens-81wgbxk8olpk/v1",
"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": "2024-10-25T04:18:36.482573+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM0829UPAR/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0829UPAR",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-cas9-ko-gata3-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2398ZXBQ/",
"accession": "IGVFDS2398ZXBQ",
"file_set_type": "guide library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000107485/",
"geneid": "ENSG00000107485",
"name": "GATA binding protein 3",
"summary": "GATA3 - ENSG00000107485 (Homo sapiens)",
"symbol": "GATA3"
}
],
"summary": "Guide (sgRNA) library targeting transcription start sites in GATA3"
}
],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout"
}
],
"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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-09T19:25:02.113892+00:00",
"summary": "knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3",
"uuid": "f0b01f8e-29a1-4ca0-9215-5df9e7587299"
}