{
"@context": "/terms/",
"@id": "/alignment-files/IGVFFI3376UGYD/",
"@type": [
"AlignmentFile",
"File",
"Item"
],
"accession": "IGVFFI3376UGYD",
"aliases": [
"charles-gersbach:cd8-tcells-atac-seq-acute-activation-batf3-bam-rep3"
],
"analysis_step_version": "/analysis-step-versions/c95d766a-a900-4694-8065-e12651f618ba/",
"assay_titles": [
"ATAC-seq"
],
"assembly": "GRCh38",
"audit": {},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization"
},
"content_md5sum": "872f5b54e8c74aca6576e07d290e8f8f",
"content_summary": "filtered alignments",
"content_type": "alignments",
"controlled_access": false,
"creation_timestamp": "2024-10-14T21:14:54.405281+00:00",
"derived_from": [
"/sequence-files/IGVFFI7305YHHH/",
"/sequence-files/IGVFFI7213KMGV/"
],
"file_format": "bam",
"file_set": {
"@id": "/analysis-sets/IGVFDS2302NLIO/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2302NLIO",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/primary-cells/IGVFSM0293OVAT/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0293OVAT",
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_term_name": "Antibody Coated Bead"
}
]
},
{
"@id": "/primary-cells/IGVFSM8800PZZL/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8800PZZL",
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_term_name": "Antibody Coated Bead"
}
]
},
{
"@id": "/primary-cells/IGVFSM4716FORO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4716FORO",
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_term_name": "Antibody Coated Bead"
}
]
},
{
"@id": "/primary-cells/IGVFSM3998OQDA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3998OQDA",
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_term_name": "Antibody Coated Bead"
}
]
},
{
"@id": "/primary-cells/IGVFSM0066TACG/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0066TACG",
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_term_name": "Antibody Coated Bead"
}
]
},
{
"@id": "/primary-cells/IGVFSM6851CRLW/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6851CRLW",
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000909/",
"status": "released",
"term_name": "CD8-positive, alpha-beta memory T cell"
}
],
"status": "released",
"summary": "Homo sapiens CD8-positive, alpha-beta memory T cell treated with 300 percent Antibody Coated Bead, transduced (lentivirus) with a expression vector library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/725c21b1-d202-4a6c-89a4-e4fc05a001e8/",
"purpose": "stimulation",
"status": "in progress",
"summary": "Treatment of 300 percent Antibody Coated Bead",
"treatment_term_name": "Antibody Coated Bead"
}
]
}
],
"status": "released",
"summary": "ATAC-seq: alignments, fold change over control, peak quantifications"
},
"file_size": 1822140938,
"filtered": true,
"gene_list_for": [],
"href": "/alignment-files/IGVFFI3376UGYD/@@download/IGVFFI3376UGYD.bam",
"input_file_for": [
"/tabular-files/IGVFFI4701TPMH/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"loci_list_for": [],
"md5sum": "8e09c0de4c1460dc31b54a47364271ef",
"quality_metrics": [],
"read_count": 59249767,
"redacted": false,
"reference_files": [
"/reference-files/IGVFFI0653VCGH/"
],
"release_timestamp": "2024-10-29T17:33:35.892786+00:00",
"s3_uri": "s3://igvf-files/2024/10/14/20b0392e-7259-4c74-bdfe-94e3b27c8ff3/IGVFFI3376UGYD.bam",
"schema_version": "14",
"status": "released",
"submitted_by": {
"@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
"title": "Alejandro Barrera"
},
"submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/SCM-70-rep3.masked.dups_marked.bam",
"summary": "GRCh38 filtered alignments",
"upload_status": "validated",
"uuid": "20b0392e-7259-4c74-bdfe-94e3b27c8ff3",
"workflow": {
"@id": "/workflows/IGVFWF6411VZLF/",
"name": "Gersbach GGR ATAC-seq Pipeline"
}
}