IGVFDS6344XBAV

released
{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS6344XBAV/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6344XBAV",
    "aliases": [
        "charles-gersbach:cd8-tcells-analysis-set-atac-seq-chronic-activation-batf3"
    ],
    "assay_titles": [
        "ATAC-seq"
    ],
    "audit": {
        "WARNING": [
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM3805WZUU](/primary-cells/IGVFSM3805WZUU/) 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/IGVFSM3805WZUU/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM7232YAVV](/primary-cells/IGVFSM7232YAVV/) 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/IGVFSM7232YAVV/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM8821YQXI](/primary-cells/IGVFSM8821YQXI/) 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/IGVFSM8821YQXI/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM6508DFUL](/primary-cells/IGVFSM6508DFUL/) 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/IGVFSM6508DFUL/"
            }
        ]
    },
    "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/IGVFDS5584SPIV/",
            "accession": "IGVFDS5584SPIV",
            "file_set_type": "expression vector library",
            "status": "released",
            "summary": "control transduction expression vector library"
        },
        {
            "@id": "/construct-library-sets/IGVFDS1868WXHB/",
            "accession": "IGVFDS1868WXHB",
            "file_set_type": "expression vector library",
            "status": "released",
            "summary": "expression vector library of BATF3"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-08-30T18:03:12.976623+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1522NSLA/",
            "accession": "IGVFDO1522NSLA",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-10"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO9588OERW/",
            "accession": "IGVFDO9588OERW",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-9"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
    "files": [
        {
            "@id": "/tabular-files/IGVFFI0911IUZS/",
            "accession": "IGVFFI0911IUZS",
            "aliases": [
                "charles-gersbach:cd8-tcells-deseq2-results-atac-seq-chronic-activation"
            ],
            "assembly": "GRCh38",
            "content_type": "fold change over control",
            "controlled_access": false,
            "creation_timestamp": "2024-09-05T20:40:11.660473+00:00",
            "file_format": "tsv",
            "file_size": 4226280,
            "href": "/tabular-files/IGVFFI0911IUZS/@@download/IGVFFI0911IUZS.tsv.gz",
            "s3_uri": "s3://igvf-files/2024/09/05/567830c6-72f5-4a23-b1d6-36b706c98388/IGVFFI0911IUZS.tsv.gz",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/DESeq2.BATF3.vs.control.acute.simple.txt.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI4762WUEH/",
            "accession": "IGVFFI4762WUEH",
            "aliases": [
                "charles-gersbach:cd8-tcells-counts-atac-seq-chronic-activation"
            ],
            "assembly": "GRCh38",
            "content_type": "peak quantifications",
            "controlled_access": false,
            "creation_timestamp": "2024-09-20T18:54:01.005667+00:00",
            "file_format": "tsv",
            "file_size": 2200810,
            "href": "/tabular-files/IGVFFI4762WUEH/@@download/IGVFFI4762WUEH.tsv.gz",
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            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8_tcells.chronic_activation_batf3.atacseq.counts.txt.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/alignment-files/IGVFFI5684XZYN/",
            "accession": "IGVFFI5684XZYN",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-bam-rep2"
            ],
            "assembly": "GRCh38",
            "content_type": "alignments",
            "controlled_access": false,
            "creation_timestamp": "2024-10-14T21:07:35.491147+00:00",
            "file_format": "bam",
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            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/alignment-files/IGVFFI4926QIFF/",
            "accession": "IGVFFI4926QIFF",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-bam-rep1"
            ],
            "assembly": "GRCh38",
            "content_type": "alignments",
            "controlled_access": false,
            "creation_timestamp": "2024-10-14T21:06:40.648784+00:00",
            "file_format": "bam",
            "file_size": 1529837023,
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            "s3_uri": "s3://igvf-files/2024/10/14/5a560ef4-79c5-4256-88f8-0a39f3c458f0/IGVFFI4926QIFF.bam",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C69-rep1.masked.dups_marked.bam",
            "upload_status": "validated"
        },
        {
            "@id": "/alignment-files/IGVFFI9649KWTN/",
            "accession": "IGVFFI9649KWTN",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-bam-rep2"
            ],
            "assembly": "GRCh38",
            "content_type": "alignments",
            "controlled_access": false,
            "creation_timestamp": "2024-10-14T21:09:30.432955+00:00",
            "file_format": "bam",
            "file_size": 1923865155,
            "href": "/alignment-files/IGVFFI9649KWTN/@@download/IGVFFI9649KWTN.bam",
            "s3_uri": "s3://igvf-files/2024/10/14/be800da9-b7a6-4899-95f6-90111c7bb2e4/IGVFFI9649KWTN.bam",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C70-rep2.masked.dups_marked.bam",
            "upload_status": "validated"
        },
        {
            "@id": "/alignment-files/IGVFFI2041YQHB/",
            "accession": "IGVFFI2041YQHB",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-bam-rep1"
            ],
            "assembly": "GRCh38",
            "content_type": "alignments",
            "controlled_access": false,
            "creation_timestamp": "2024-10-14T21:08:31.217342+00:00",
            "file_format": "bam",
            "file_size": 1873245689,
            "href": "/alignment-files/IGVFFI2041YQHB/@@download/IGVFFI2041YQHB.bam",
            "s3_uri": "s3://igvf-files/2024/10/14/b63932d4-d1a8-4880-84f8-911b0b77f110/IGVFFI2041YQHB.bam",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-C70-rep1.masked.dups_marked.bam",
            "upload_status": "validated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0986HRDF/",
            "accession": "IGVFDS0986HRDF",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-rep1"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS5328ZNKL/",
            "accession": "IGVFDS5328ZNKL",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-batf3-rep2"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS3810SJRN/",
            "accession": "IGVFDS3810SJRN",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-rep1"
            ],
            "file_set_type": "experimental data",
            "status": "released"
        },
        {
            "@id": "/measurement-sets/IGVFDS9111EVGC/",
            "accession": "IGVFDS9111EVGC",
            "aliases": [
                "charles-gersbach:cd8-tcells-atac-seq-chronic-activation-gfp-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/atac-seq-primary-human-t-cells-overexpressing-batf-c5pfy5jn"
    ],
    "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": "2024-10-29T17:33:32.536556+00:00",
    "sample_summary": "CD8-positive, alpha-beta memory T primary cell primary cell, transfected with a expression vector library",
    "samples": [
        {
            "@id": "/primary-cells/IGVFSM3805WZUU/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3805WZUU",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-chronic-activation-gfp-rep2"
            ],
            "classifications": [
                "primary cell"
            ],
            "institutional_certificates": [
                {
                    "@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
                    "certificate_identifier": "IP117-01",
                    "controlled_access": false,
                    "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": "CD8-positive, alpha-beta memory T cell, Homo sapiens transduced (lentivirus) with a expression vector library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/primary-cells/IGVFSM8821YQXI/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8821YQXI",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep1"
            ],
            "classifications": [
                "primary cell"
            ],
            "institutional_certificates": [
                {
                    "@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
                    "certificate_identifier": "IP117-01",
                    "controlled_access": false,
                    "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": "CD8-positive, alpha-beta memory T cell, Homo sapiens transduced (lentivirus) with a expression vector library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/primary-cells/IGVFSM7232YAVV/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7232YAVV",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-chronic-activation-batf3-rep2"
            ],
            "classifications": [
                "primary cell"
            ],
            "institutional_certificates": [
                {
                    "@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
                    "certificate_identifier": "IP117-01",
                    "controlled_access": false,
                    "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": "CD8-positive, alpha-beta memory T cell, Homo sapiens transduced (lentivirus) with a expression vector library",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/primary-cells/IGVFSM6508DFUL/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6508DFUL",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-chronic-activation-gfp-rep1"
            ],
            "classifications": [
                "primary cell"
            ],
            "institutional_certificates": [
                {
                    "@id": "/institutional-certificates/e1533003-0a58-47b1-aa1a-615dbb6aafb2/",
                    "certificate_identifier": "IP117-01",
                    "controlled_access": false,
                    "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": "CD8-positive, alpha-beta memory T cell, Homo sapiens transduced (lentivirus) with a expression vector library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2024-09-05T20:40:11.660473+00:00",
    "summary": "ATAC-seq: alignments, fold change over control, peak quantifications",
    "uuid": "fcdc0263-c1e7-4ba0-87ba-5bcbfef7461c",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF6411VZLF/",
            "accession": "IGVFWF6411VZLF",
            "name": "Gersbach GGR ATAC-seq Pipeline",
            "status": "released"
        }
    ]
}