{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS0320JXJG/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0320JXJG",
"aliases": [
"charles-gersbach:cd8-tcells-analysis-set-crispra-ccr7"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4110AXZO](/primary-cells/IGVFSM4110AXZO/) 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/IGVFSM4110AXZO/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM8964QQSX](/primary-cells/IGVFSM8964QQSX/) 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/IGVFSM8964QQSX/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1721KPGX](/primary-cells/IGVFSM1721KPGX/) 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/IGVFSM1721KPGX/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7634EVUP](/primary-cells/IGVFSM7634EVUP/) 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/IGVFSM7634EVUP/"
},
{
"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 age",
"detail": "Primary cell [IGVFSM7418TTPB](/primary-cells/IGVFSM7418TTPB/) 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/IGVFSM7418TTPB/"
}
]
},
"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": [],
"creation_timestamp": "2024-08-28T21:06:22.334319+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO4579FYIL/",
"accession": "IGVFDO4579FYIL",
"aliases": [
"charles-gersbach:cd8-tcells-donor-22"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3231VPAA/",
"accession": "IGVFDO3231VPAA",
"aliases": [
"charles-gersbach:cd8-tcells-donor-20"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO5479ZYLJ/",
"accession": "IGVFDO5479ZYLJ",
"aliases": [
"charles-gersbach:cd8-tcells-donor-21"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI5185FVQD/",
"accession": "IGVFFI5185FVQD",
"aliases": [
"charles-gersbach:cd8-tcells-guide-counts-crispra-ccr7"
],
"assembly": "custom",
"content_type": "guide quantifications",
"controlled_access": false,
"creation_timestamp": "2024-09-20T18:40:01.344785+00:00",
"file_format": "csv",
"file_size": 47877,
"href": "/tabular-files/IGVFFI5185FVQD/@@download/IGVFFI5185FVQD.csv.gz",
"s3_uri": "s3://igvf-files/2024/09/20/113b3bf4-6732-4f48-a5eb-6d23ebfb514e/IGVFFI5185FVQD.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRa.TF.CCR7.counts.table.csv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1152VRSY/",
"accession": "IGVFFI1152VRSY",
"aliases": [
"charles-gersbach:cd8-tcells-guide-quantifications-crispra-ccr7"
],
"assembly": "custom",
"content_type": "fold change over control",
"controlled_access": false,
"creation_timestamp": "2024-09-05T20:41:59.339100+00:00",
"file_format": "tsv",
"file_size": 73393,
"href": "/tabular-files/IGVFFI1152VRSY/@@download/IGVFFI1152VRSY.tsv.gz",
"s3_uri": "s3://igvf-files/2024/09/05/7dd18684-e84e-4e26-b7c3-746099a13fdc/IGVFFI1152VRSY.tsv.gz",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T2D_DESeq2_CRISPRa_TF_screen.simple.v2.txt.gz",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI0042LTLO/",
"accession": "IGVFFI0042LTLO",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:57:35.089042+00:00",
"file_format": "bam",
"file_size": 15731832,
"href": "/alignment-files/IGVFFI0042LTLO/@@download/IGVFFI0042LTLO.bam",
"s3_uri": "s3://igvf-files/2024/10/15/8b62c47d-4406-48db-8ba4-c89c073fe816/IGVFFI0042LTLO.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-L1_S5.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI3803FGJT/",
"accession": "IGVFFI3803FGJT",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:58:20.257334+00:00",
"file_format": "bam",
"file_size": 9715009,
"href": "/alignment-files/IGVFFI3803FGJT/@@download/IGVFFI3803FGJT.bam",
"s3_uri": "s3://igvf-files/2024/10/15/e0325d33-75e4-42ff-a837-4997e1c96103/IGVFFI3803FGJT.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-L2_S7.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5368ITLJ/",
"accession": "IGVFFI5368ITLJ",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:03:41.808532+00:00",
"file_format": "bam",
"file_size": 43997867,
"href": "/alignment-files/IGVFFI5368ITLJ/@@download/IGVFFI5368ITLJ.bam",
"s3_uri": "s3://igvf-files/2024/10/15/e3e3105f-88d6-4716-8656-17f3bd3ef08d/IGVFFI5368ITLJ.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-H2_S8.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI5953CWOK/",
"accession": "IGVFFI5953CWOK",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-low-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T18:58:46.328862+00:00",
"file_format": "bam",
"file_size": 37391338,
"href": "/alignment-files/IGVFFI5953CWOK/@@download/IGVFFI5953CWOK.bam",
"s3_uri": "s3://igvf-files/2024/10/15/ca129491-5544-4ad0-af35-87953bec7dc8/IGVFFI5953CWOK.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-L3_S9.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI6968CHOY/",
"accession": "IGVFFI6968CHOY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-high-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:04:08.323341+00:00",
"file_format": "bam",
"file_size": 20790338,
"href": "/alignment-files/IGVFFI6968CHOY/@@download/IGVFFI6968CHOY.bam",
"s3_uri": "s3://igvf-files/2024/10/15/aa620f9a-2aaa-4b25-9305-8066a5cc13c4/IGVFFI6968CHOY.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-H3_S10.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8192HFRA/",
"accession": "IGVFFI8192HFRA",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-15T19:03:15.729180+00:00",
"file_format": "bam",
"file_size": 22261021,
"href": "/alignment-files/IGVFFI8192HFRA/@@download/IGVFFI8192HFRA.bam",
"s3_uri": "s3://igvf-files/2024/10/15/a52dbbba-f1f3-4b98-b105-79c0ef588e17/IGVFFI8192HFRA.bam",
"status": "released",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-H1_S6.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS8981FZRC/",
"accession": "IGVFDS8981FZRC",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6164ZDND/",
"accession": "IGVFDS6164ZDND",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6262JHMS/",
"accession": "IGVFDS6262JHMS",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5417LSWU/",
"accession": "IGVFDS5417LSWU",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6373KKOW/",
"accession": "IGVFDS6373KKOW",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5281AOTI/",
"accession": "IGVFDS5281AOTI",
"aliases": [
"charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep2"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"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": "2024-11-18T21:08:52.356369+00:00",
"sample_summary": "Homo sapiens CD8-positive, alpha-beta memory T primary cell primary cell, modified with CRISPRa Sa-dCas9-VP64, transfected with a guide library, sorted on expression of CCR7",
"samples": [
{
"@id": "/primary-cells/IGVFSM1721KPGX/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1721KPGX",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep3"
],
"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 90-100% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7418TTPB/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7418TTPB",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-low-bin-rep1"
],
"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"
},
{
"@id": "/primary-cells/IGVFSM4110AXZO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4110AXZO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-low-bin-rep3"
],
"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"
},
{
"@id": "/primary-cells/IGVFSM8964QQSX/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8964QQSX",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep1"
],
"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 90-100% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7634EVUP/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7634EVUP",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-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 90-100% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@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": "9",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_files_timestamp": "2024-09-05T20:41:59.339100+00:00",
"summary": "CRISPR activation FACS screen targeting CCR7: alignments, fold change over control, guide quantifications",
"uuid": "f42d6b34-7961-4abb-be67-24603b5792dc",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow",
"status": "released"
}
]
}