{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4663XDBF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4663XDBF",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-low-bin-rep3"
],
"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 [IGVFDS4663XDBF](/measurement-sets/IGVFDS4663XDBF/) has sequence file(s): [IGVFFI2791EHZO](/sequence-files/IGVFFI2791EHZO/) 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/IGVFDS4663XDBF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4663XDBF](/measurement-sets/IGVFDS4663XDBF/) 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/IGVFDS4663XDBF/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM6350DJQS](/primary-cells/IGVFSM6350DJQS/) 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/IGVFSM6350DJQS/"
}
]
},
"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/IGVFDS8345ZMZW/",
"accession": "IGVFDS8345ZMZW",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI0477HTCF/",
"accession": "IGVFFI0477HTCF",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting transcription start sites in CD2"
}
],
"control_for": [
{
"@id": "/measurement-sets/IGVFDS5951POJU/",
"accession": "IGVFDS5951POJU",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-high-bin-rep3"
],
"status": "released"
}
],
"control_type": "low FACS signal",
"creation_timestamp": "2023-11-08T19:32:27.315839+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1423VLXL/",
"accession": "IGVFDO1423VLXL",
"aliases": [
"charles-gersbach:cd8-tcells-donor-16"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2791EHZO/",
"accession": "IGVFFI2791EHZO",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-low-bin-rep3-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-11-08T20:27:22.715991+00:00",
"file_format": "fastq",
"file_size": 33730039,
"href": "/sequence-files/IGVFFI2791EHZO/@@download/IGVFFI2791EHZO.fastq.gz",
"md5sum": "f01eec600531e7455c58d39438027dbd",
"s3_uri": "s3://igvf-files/2023/11/08/e0614745-755c-4af2-81e6-b0d769d12371/IGVFFI2791EHZO.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/pSM8-Low-R3_S16_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5157TBYH/"
],
"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/crispri-tiling-screens-c5rby52n"
],
"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": "2024-11-19T20:35:03.475266+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM6350DJQS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6350DJQS",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-low-bin-rep3"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference",
"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 CD2) modified with CRISPRi Sa-dCas9-KOX1-KRAB, 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": "2023-11-08T20:27:22.715991+00:00",
"summary": "low FACS signal CRISPR interference FACS screen sorted on the expression of CD2 integrating a guide (sgRNA) library targeting transcription start sites in CD2",
"targeted_genes": [
{
"@id": "/genes/ENSG00000116824/",
"geneid": "ENSG00000116824",
"name": "CD2 molecule",
"status": "released",
"symbol": "CD2",
"synonyms": [
"T-cell surface antigen T11/Leu-5",
"SRBC",
"LFA-3 receptor",
"T11",
"erythrocyte receptor",
"CD2",
"rosette receptor",
"CD2 molecule",
"LFA-2",
"CD2 antigen (p50), sheep red blood cell receptor",
"T-cell surface antigen CD2",
"lymphocyte-function antigen-2"
]
}
],
"uuid": "9c23aade-1af8-4a05-a8af-7e82f4540e16"
}