{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5281AOTI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5281AOTI",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep2"
],
"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 [IGVFDS5281AOTI](/measurement-sets/IGVFDS5281AOTI/) has sequence file(s): [IGVFFI5864HMZJ](/sequence-files/IGVFFI5864HMZJ/) 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/IGVFDS5281AOTI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6002TGBI](/primary-cells/IGVFSM6002TGBI/) 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/IGVFSM6002TGBI/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5281AOTI](/measurement-sets/IGVFDS5281AOTI/) 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/IGVFDS5281AOTI/"
}
]
},
"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/IGVFDS4163YHBI/",
"accession": "IGVFDS4163YHBI",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI6308XVUC/",
"accession": "IGVFFI6308XVUC",
"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"
}
],
"control_for": [
{
"@id": "/measurement-sets/IGVFDS8981FZRC/",
"accession": "IGVFDS8981FZRC",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep2"
],
"status": "released"
}
],
"control_type": "low FACS signal",
"creation_timestamp": "2023-11-08T19:32:44.786162+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO5479ZYLJ/",
"accession": "IGVFDO5479ZYLJ",
"aliases": [
"charles-gersbach:cd8-tcells-donor-21"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5864HMZJ/",
"accession": "IGVFFI5864HMZJ",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:30:59.209914+00:00",
"file_format": "fastq",
"file_size": 13565060,
"href": "/sequence-files/IGVFFI5864HMZJ/@@download/IGVFFI5864HMZJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/11/08/d2d8b1d8-9afb-4263-8e4d-ef907be465ab/IGVFFI5864HMZJ.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/CCR7pos-pSM54-TF-L2_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0320JXJG/"
],
"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": "2024-11-19T20:34:43.374759+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM6002TGBI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6002TGBI",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation",
"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 CCR7) modified with CRISPRa Sa-dCas9-VP64, 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": "2023-11-08T20:30:59.209914+00:00",
"summary": "low FACS signal CRISPR activation FACS screen sorted on the expression of CCR7 integrating a guide (sgRNA) library targeting transcription start sites in many genes",
"targeted_genes": [
{
"@id": "/genes/ENSG00000126353/",
"geneid": "ENSG00000126353",
"name": "C-C motif chemokine receptor 7",
"status": "released",
"symbol": "CCR7",
"synonyms": [
"EBI1",
"CC chemokine receptor 7",
"BLR2",
"CCR-7",
"Epstein-Barr virus-induced G-protein coupled receptor 1",
"CC-CKR-7",
"lymphocyte-specific G protein-coupled peptide receptor",
"Epstein-Barr virus induced gene 1",
"Bukitt's lymphoma receptor 2",
"CDw197",
"chemokine (C-C motif) receptor 7",
"C-C chemokine receptor type 7",
"C-C motif chemokine receptor 7",
"MIP-3 beta receptor",
"CCR7",
"CD197",
"EBV-induced G protein-coupled receptor 1",
"CMKBR7"
]
}
],
"uuid": "552ee6eb-fffd-4efb-86c7-8f976c75a090"
}