{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3910ZTSZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3910ZTSZ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-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 [IGVFDS3910ZTSZ](/measurement-sets/IGVFDS3910ZTSZ/) has sequence file(s): [IGVFFI7351KKAC](/sequence-files/IGVFFI7351KKAC/) 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/IGVFDS3910ZTSZ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM3895SURE](/primary-cells/IGVFSM3895SURE/) 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/IGVFSM3895SURE/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3910ZTSZ](/measurement-sets/IGVFDS3910ZTSZ/) 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/IGVFDS3910ZTSZ/"
}
]
},
"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/IGVFDS3667PLQB/",
"accession": "IGVFDS3667PLQB",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9735DZKB/",
"accession": "IGVFFI9735DZKB",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in many genes"
},
{
"@id": "/construct-library-sets/IGVFDS1868WXHB/",
"accession": "IGVFDS1868WXHB",
"file_set_type": "expression vector library",
"status": "released",
"summary": "expression vector library of BATF3"
}
],
"control_for": [
{
"@id": "/measurement-sets/IGVFDS2160ZTSJ/",
"accession": "IGVFDS2160ZTSJ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-high-bin-rep1"
],
"status": "released"
}
],
"control_type": "low FACS signal",
"creation_timestamp": "2023-11-08T19:32:40.882202+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8306NDTY/",
"accession": "IGVFDO8306NDTY",
"aliases": [
"charles-gersbach:cd8-tcells-donor-25"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7351KKAC/",
"accession": "IGVFFI7351KKAC",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep1-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:29:59.117201+00:00",
"file_format": "fastq",
"file_size": 549544531,
"href": "/sequence-files/IGVFFI7351KKAC/@@download/IGVFFI7351KKAC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/3e909f0e-bd99-41b1-ac2a-37495af831a9/IGVFFI7351KKAC.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/pSM74_L2_S8_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8364HJHL/"
],
"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/tfome-crisprko-screens-81wgbxk8olpk/v1"
],
"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": "2024-11-19T20:34:38.049860+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM3895SURE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3895SURE",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
"modality": "knockout",
"status": "released"
}
],
"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": "Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 0-10% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (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": "2023-11-08T20:29:59.117201+00:00",
"summary": "low FACS signal CRISPR knockout FACS screen sorted on the expression of IL7R integrating an expression vector library of BATF3 and a guide (sgRNA) library targeting transcription start sites in many genes",
"targeted_genes": [
{
"@id": "/genes/ENSG00000168685/",
"geneid": "ENSG00000168685",
"name": "interleukin 7 receptor",
"status": "released",
"symbol": "IL7R",
"synonyms": [
"IL-7R-alpha",
"ILRA",
"IMD104",
"lnc-IL7R",
"IL7Ralpha",
"IL-7 receptor subunit alpha",
"CDW127",
"sIL-7R",
"interleukin-7 receptor subunit alpha",
"CD127",
"CD127 antigen",
"IL-7R subunit alpha",
"soluble interleukin-7 receptor",
"IL-7Ralpha",
"IL7R",
"interleukin 7 receptor alpha chain",
"IL7RA",
"interleukin 7 receptor"
]
}
],
"uuid": "507a0f56-e2b7-455f-9aa5-a75caaf1bf7a"
}