{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4488GLKL/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4488GLKL",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispra-ccr7"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"WARNING": [
{
"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/"
},
{
"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 [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/"
}
]
},
"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"
},
"control_for": [],
"creation_timestamp": "2024-09-20T15:06:26.697792+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/IGVFDO5479ZYLJ/",
"accession": "IGVFDO5479ZYLJ",
"aliases": [
"charles-gersbach:cd8-tcells-donor-21"
],
"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"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/IGVFFI3803FGJT/",
"accession": "IGVFFI3803FGJT",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"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",
"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",
"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",
"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/IGVFFI6968CHOY/",
"accession": "IGVFFI6968CHOY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-high-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"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",
"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/IGVFFI0042LTLO/",
"accession": "IGVFFI0042LTLO",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"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",
"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/IGVFFI5953CWOK/",
"accession": "IGVFFI5953CWOK",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-low-bin-rep3"
],
"assembly": "custom",
"content_type": "alignments",
"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",
"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/IGVFFI8192HFRA/",
"accession": "IGVFFI8192HFRA",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispra-ccr7-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"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",
"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": "/auxiliary-sets/IGVFDS5903JKGX/",
"accession": "IGVFDS5903JKGX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-low-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS5759ZVUX/",
"accession": "IGVFDS5759ZVUX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-low-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS6878SUMX/",
"accession": "IGVFDS6878SUMX",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-low-bin-rep3"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS7251RDFD/",
"accession": "IGVFDS7251RDFD",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-high-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS9073AJJA/",
"accession": "IGVFDS9073AJJA",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-high-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS9310VIMF/",
"accession": "IGVFDS9310VIMF",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-high-bin-rep3"
],
"file_set_type": "gRNA sequencing"
}
],
"input_for": [
"/analysis-sets/IGVFDS0320JXJG/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"protocols": [],
"publications": [
{
"@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
"publication_identifiers": [
"PMID:37945901",
"doi:10.1038/s41588-023-01554-0",
"PMCID:PMC10703699"
]
}
],
"release_timestamp": "2024-11-18T21:08:52.567734+00:00",
"sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, modified with CRISPR modifications, transfected with a guide library, sorted on expression of CCR7",
"samples": [
{
"@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"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens (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/IGVFSM7634EVUP/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7634EVUP",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens (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/IGVFSM1721KPGX/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1721KPGX",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep3"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens (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/IGVFSM8964QQSX/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8964QQSX",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens (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"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens (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/IGVFSM7418TTPB/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7418TTPB",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
"modality": "activation"
}
],
"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": "CD8-positive, alpha-beta memory T cell, Homo sapiens (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": "2024-10-15T18:57:35.089042+00:00",
"summary": "CRISPR activation FACS screen targeting CCR7: alignments",
"uuid": "cb6bfc95-81ab-4c2e-9fa5-a0b8ddbeb1dd",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow"
}
]
}