{
"@context": "/terms/",
"@id": "/matrix-files/IGVFFI3108PBUQ/",
"@type": [
"MatrixFile",
"File",
"Item"
],
"accession": "IGVFFI3108PBUQ",
"aliases": [
"jay-shendure:matrixfile_CREs_scATAC_PeaksByCellCountMatrix_LaLanne"
],
"analysis_step_version": "/analysis-step-versions/4b52b7fa-e00e-4fc8-b653-ab0ca32174ba/",
"assay_titles": [
"scATAC-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI3108PBUQ](/matrix-files/IGVFFI3108PBUQ/) has in progress subobject analysis step version [4b52b7fa-e00e-4fc8-b653-ab0ca32174ba](/analysis-step-versions/4b52b7fa-e00e-4fc8-b653-ab0ca32174ba/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI3108PBUQ/"
}
]
},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization"
},
"checkfiles_version": "v16",
"content_md5sum": "eaf65943d1c64e3d43c5099587afb73d",
"content_summary": "cell by peak in sparse peak count matrix",
"content_type": "sparse peak count matrix",
"creation_timestamp": "2024-12-18T19:06:25.278943+00:00",
"derived_from": [
"/tabular-files/IGVFFI9775SYBY/"
],
"file_format": "mtx",
"file_format_specifications": [
"/documents/264040c5-4f62-45a7-bbc1-1f78a979d833/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS7801YPEU/",
"accession": "IGVFDS7801YPEU",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4284RDJK/",
"accession": "IGVFSM4284RDJK",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0004038/",
"status": "released",
"term_name": "mouse embryonic stem cell"
}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10XlaneB), male, Mus musculus WD44",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM6820XJKR/",
"accession": "IGVFSM6820XJKR",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0004038/",
"status": "released",
"term_name": "mouse embryonic stem cell"
}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10XlaneB), male, Mus musculus WD44",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM9475FJUV/",
"accession": "IGVFSM9475FJUV",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0004038/",
"status": "released",
"term_name": "mouse embryonic stem cell"
}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10XlaneA), male, Mus musculus WD44",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
},
{
"@id": "/in-vitro-systems/IGVFSM7126ZMPT/",
"accession": "IGVFSM7126ZMPT",
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0004038/",
"status": "released",
"term_name": "mouse embryonic stem cell"
}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10XlaneA), male, Mus musculus WD44",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"status": "released",
"summary": "scATAC-seq: fragments, peaks, signal, sparse peak count matrix"
},
"file_size": 470296214,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI3108PBUQ/@@download/IGVFFI3108PBUQ.mtx.gz",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"loci_list_for": [],
"md5sum": "34cc6470486fd6dddfdcd2cc79dba8a6",
"principal_dimension": "cell",
"quality_metrics": [],
"reference_files": [
"/reference-files/IGVFFI9282QLXO/"
],
"release_timestamp": "2025-02-19T21:45:55.955798+00:00",
"s3_uri": "s3://igvf-files/2024/12/18/52e2de14-1442-4b55-83a2-4bff17e31de1/IGVFFI3108PBUQ.mtx",
"schema_version": "7",
"secondary_dimensions": [
"peak"
],
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/scQers/peak_by_cell_matrix_exported_ArchR_PeakMatrix_mEB_day21_20241120.mtx.gz",
"summary": "cell by peak in sparse peak count matrix",
"upload_status": "validated",
"uuid": "52e2de14-1442-4b55-83a2-4bff17e31de1",
"workflow": {
"@id": "/workflows/IGVFWF7196TNJP/",
"name": "Shendure scATAC-seq Pipeline",
"uniform_pipeline": false
}
}