{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9065THHI/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9065THHI",
"aliases": [
"charles-gersbach:cd8-tcells-intermediate-analysis-crispri-ccr7"
],
"assay_titles": [
"CRISPR FACS screen"
],
"audit": {
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2207SJEN](/primary-cells/IGVFSM2207SJEN/) 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/IGVFSM2207SJEN/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM9398LTWW](/primary-cells/IGVFSM9398LTWW/) 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/IGVFSM9398LTWW/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7413JCSK](/primary-cells/IGVFSM7413JCSK/) 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/IGVFSM7413JCSK/"
},
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1205VMNO](/primary-cells/IGVFSM1205VMNO/) 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/IGVFSM1205VMNO/"
}
]
},
"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": "2024-09-20T15:06:20.927733+00:00",
"donors": [
{
"@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/IGVFFI7658XOUY/",
"accession": "IGVFFI7658XOUY",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-ccr7-high-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:59:21.594747+00:00",
"file_format": "bam",
"file_size": 13972258,
"href": "/alignment-files/IGVFFI7658XOUY/@@download/IGVFFI7658XOUY.bam",
"s3_uri": "s3://igvf-files/2024/10/15/7ecff3f4-5e98-4d37-8121-c79cffe3f0f9/IGVFFI7658XOUY.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM27-TF-H1_S2.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI1939MBPM/",
"accession": "IGVFFI1939MBPM",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-ccr7-high-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:59:49.372589+00:00",
"file_format": "bam",
"file_size": 56018812,
"href": "/alignment-files/IGVFFI1939MBPM/@@download/IGVFFI1939MBPM.bam",
"s3_uri": "s3://igvf-files/2024/10/15/bb8e188c-ddce-4f43-b535-1e1ee030e75e/IGVFFI1939MBPM.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM27-TF-H3_S4.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI8745XXNE/",
"accession": "IGVFFI8745XXNE",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-ccr7-low-bin-rep2"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:54:14.573254+00:00",
"file_format": "bam",
"file_size": 9493128,
"href": "/alignment-files/IGVFFI8745XXNE/@@download/IGVFFI8745XXNE.bam",
"s3_uri": "s3://igvf-files/2024/10/15/133739de-25d4-47af-a803-31a9aae2a3f9/IGVFFI8745XXNE.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM27-TF-L3_S3.sorted.bam",
"upload_status": "validated"
},
{
"@id": "/alignment-files/IGVFFI6752WOMF/",
"accession": "IGVFFI6752WOMF",
"aliases": [
"charles-gersbach:cd8-tcells-alignment-crispri-ccr7-low-bin-rep1"
],
"assembly": "custom",
"content_type": "alignments",
"creation_timestamp": "2024-10-15T18:53:38.750503+00:00",
"file_format": "bam",
"file_size": 35675159,
"href": "/alignment-files/IGVFFI6752WOMF/@@download/IGVFFI6752WOMF.bam",
"s3_uri": "s3://igvf-files/2024/10/15/eddff917-3f98-4e9c-8e38-58dcf0c7fc6c/IGVFFI6752WOMF.bam",
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CCR7pos-pSM27-TF-L1_S1.sorted.bam",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9693EKGR/",
"accession": "IGVFDS9693EKGR",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-ccr7-low-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS5825GTXD/",
"accession": "IGVFDS5825GTXD",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-ccr7-low-bin-rep2"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS3536DHAB/",
"accession": "IGVFDS3536DHAB",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-ccr7-high-bin-rep1"
],
"file_set_type": "gRNA sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS6547DKWF/",
"accession": "IGVFDS6547DKWF",
"aliases": [
"charles-gersbach:cd8-tcells-auxiliary-set-crispri-ccr7-high-bin-rep2"
],
"file_set_type": "gRNA sequencing"
}
],
"input_for": [
"/analysis-sets/IGVFDS9143TFRW/"
],
"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": "2024-11-18T21:09:09.004657+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/IGVFSM2207SJEN/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2207SJEN",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-ccr7-high-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM9398LTWW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9398LTWW",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-ccr7-low-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM7413JCSK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7413JCSK",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-ccr7-low-bin-rep1"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
"taxa": "Homo sapiens"
},
{
"@id": "/primary-cells/IGVFSM1205VMNO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1205VMNO",
"aliases": [
"charles-gersbach:cd8-tcells-primary-cell-crispri-ccr7-high-bin-rep2"
],
"classifications": [
"primary cell"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS4163YHBI/"
],
"modifications": [
{
"@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
"modality": "interference"
}
],
"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 CRISPRi Sa-dCas9, 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": "2024-10-15T18:53:38.750503+00:00",
"summary": "CRISPR interference FACS screen targeting CCR7: alignments",
"uuid": "41938c16-c0d4-4869-92a3-5103c2d6260f",
"workflows": [
{
"@id": "/workflows/IGVFWF8837BHJV/",
"accession": "IGVFWF8837BHJV",
"name": "Gersbach FACS CRISPR screen workflow"
}
]
}