{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7828ZYHS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7828ZYHS",
"aliases": [
"charles-gersbach:jurkats-auxiliary-set-crispra-vp64x2-il2ra-high-bin-rep3"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7828ZYHS](/auxiliary-sets/IGVFDS7828ZYHS/) has sequence file(s): [IGVFFI3996QKGU](/sequence-files/IGVFFI3996QKGU/) 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/IGVFDS7828ZYHS/"
}
]
},
"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": "2024-02-05T22:40:34.398135+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4048MCTZ/",
"accession": "IGVFDO4048MCTZ",
"aliases": [
"charles-gersbach:jurkat-tcells-donor-6"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3996QKGU/",
"accession": "IGVFFI3996QKGU",
"aliases": [
"charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-high-bin-rep3-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:35:43.481081+00:00",
"file_format": "fastq",
"file_size": 25551918,
"href": "/sequence-files/IGVFFI3996QKGU/@@download/IGVFFI3996QKGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/b5cccd6e-8f59-472c-8ac7-7537f301ca4d/IGVFFI3996QKGU.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/pSM26-High-R3_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5218AVPW/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5910YZFG/",
"accession": "IGVFDS5910YZFG",
"aliases": [
"charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-high-bin-rep3"
],
"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": "2024-11-18T21:08:59.330134+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3244YHOI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3244YHOI",
"aliases": [
"charles-gersbach:jurkats-in-vitro-system-crispra-vp64x2-il2ra-high-bin-rep3"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS8183QSJO/"
],
"modifications": [
{
"@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, 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": "2023-11-08T20:35:43.481081+00:00",
"summary": "gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in IL2RA",
"uuid": "4712e033-04c1-46d5-8f5b-ae7b0c239be8"
}