{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6791MFOC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6791MFOC",
"aliases": [
"charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-high-bin-rep1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6791MFOC](/measurement-sets/IGVFDS6791MFOC/) has sequence file(s): [IGVFFI3796MGXL](/sequence-files/IGVFFI3796MGXL/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6791MFOC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6791MFOC](/measurement-sets/IGVFDS6791MFOC/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS6791MFOC/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS8183QSJO/",
"accession": "IGVFDS8183QSJO",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1252VLIV/",
"accession": "IGVFFI1252VLIV",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in IL2RA"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4586UCAI/",
"accession": "IGVFDS4586UCAI",
"aliases": [
"charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-low-bin-rep1"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-08T19:33:04.861004+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3796MGXL/",
"accession": "IGVFFI3796MGXL",
"aliases": [
"charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-high-bin-rep1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:35:26.531338+00:00",
"file_format": "fastq",
"file_size": 24431052,
"href": "/sequence-files/IGVFFI3796MGXL/@@download/IGVFFI3796MGXL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/c55ec488-7e7f-41a0-a6bd-9537e34bf9b8/IGVFFI3796MGXL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004205/",
"status": "released",
"term_name": "Illumina MiSeq"
},
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM26-High-R1_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7196OWBU/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This file_set previously had 5d15ca93-89fb-4a34-8863-001eda25bb4c submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
"preferred_assay_title": "CRISPR FACS screen",
"protocols": [
"https://www.protocols.io/view/car-t-cell-characterization-by-flow-cytometry-c48qyzvw",
"https://www.protocols.io/view/crispra-tiling-screens-c5rfy53n"
],
"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": "2024-11-19T20:34:01.501542+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4817IZZH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4817IZZH",
"aliases": [
"charles-gersbach:jurkats-in-vitro-system-crispra-vp64x2-il2ra-high-bin-rep1"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) Jurkat cell line (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": "26",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2023-11-08T20:35:26.531338+00:00",
"summary": "CRISPR activation FACS screen sorted on the expression of IL2RA integrating a guide (sgRNA) library targeting transcription start sites in IL2RA",
"targeted_genes": [
{
"@id": "/genes/ENSG00000134460/",
"geneid": "ENSG00000134460",
"name": "interleukin 2 receptor subunit alpha",
"status": "released",
"symbol": "IL2RA",
"synonyms": [
"interleukin 2 receptor, alpha",
"IL-2 receptor subunit alpha",
"IL2R",
"TAC antigen",
"CD25",
"p55",
"IL-2R subunit alpha",
"TCGFR",
"interleukin-2 receptor subunit alpha",
"IMD41",
"IL2RA",
"interleukin 2 receptor subunit alpha",
"IDDM10"
]
}
],
"uuid": "483d2ef6-f64c-4910-8fec-71ba61fe43e6"
}