{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI5042DAMZ/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI5042DAMZ",
"aliases": [
"buenrostro-bernstein:IGVFDS2500WRRQ_fragments"
],
"analysis_step_version": "/analysis-step-versions/39c0498d-91f6-42de-8896-2fab1403f032/",
"assay_titles": [
"SHARE-seq"
],
"assembly": "GRCm39",
"audit": {},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping"
},
"barcode_map_for": [],
"checkfiles_version": "v20",
"content_md5sum": "a3562c40765cef35f85b5c55fb22d786",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-03-27T01:18:39.609003+00:00",
"derived_from": [
"/sequence-files/IGVFFI9289MXQE/",
"/sequence-files/IGVFFI6309QCHM/",
"/sequence-files/IGVFFI6921XINB/",
"/sequence-files/IGVFFI1056SNKD/",
"/sequence-files/IGVFFI4704XUQF/",
"/sequence-files/IGVFFI9772XBGF/",
"/sequence-files/IGVFFI9654PVVK/",
"/sequence-files/IGVFFI1441LHXN/",
"/sequence-files/IGVFFI2741WDZJ/",
"/sequence-files/IGVFFI5683TTVW/",
"/configuration-files/IGVFFI9172NVYX/",
"/configuration-files/IGVFFI9837KUMF/",
"/configuration-files/IGVFFI2731URZQ/",
"/configuration-files/IGVFFI7549SZFK/",
"/configuration-files/IGVFFI8153CPRN/"
],
"file_format": "bed",
"file_format_specifications": [
{
"@id": "/documents/db2a6dd0-cc1d-439e-a610-f9f1d04cfd82/",
"description": "Specification of fragment file generated by https://github.com/IGVF/single-cell-pipeline"
}
],
"file_format_type": "bed3+",
"file_set": {
"@id": "/analysis-sets/IGVFDS2500WRRQ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2500WRRQ",
"data_use_limitation_summaries": [
"no certificate"
],
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/tissues/IGVFSM9503WHHQ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9503WHHQ",
"classifications": [
"tissue"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"status": "released",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 433)",
"taxa": "Mus musculus"
}
],
"status": "released",
"summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)"
},
"file_size": 1358161722,
"filtered": false,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI5042DAMZ/@@download/IGVFFI5042DAMZ.bed.gz",
"input_file_for": [
"/index-files/IGVFFI6822VPWM/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"loci_list_for": [],
"md5sum": "7ccafa48438aa05cc57dfdb209e7fb62",
"primer_design_for": [],
"quality_metrics": [
"/single-cell-atac-seq-quality-metrics/293e97b8-aaab-4f27-b0eb-b8a189b79520/"
],
"release_timestamp": "2025-05-07T20:35:07.497236+00:00",
"s3_uri": "s3://igvf-files/2025/03/27/84936cbd-88bc-434f-a4d3-a5c01d6f43c0/IGVFFI5042DAMZ.bed.gz",
"schema_version": "15",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/37c6f33e-77c3-4424-9360-fe4be37474a2/call-atac/wf_atac/7a2fe1c0-7261-4735-aaa4-246d3f946892/call-generate_fragments/SS-PKR-433.fragments.tsv.gz",
"summary": "GRCm39 unfiltered fragments",
"upload_status": "validated",
"uuid": "84936cbd-88bc-434f-a4d3-a5c01d6f43c0",
"workflow": {
"@id": "/workflows/IGVFWF7365VWQV/",
"name": "igvf single cell uniform pipeline",
"uniform_pipeline": true
}
}