7 files

Single-nuclei ATAC-Seq data from human atherosclerosis

Version 2 2021-04-29, 09:45
Version 1 2021-04-29, 09:05
posted on 2021-04-29, 09:45 authored by Tiit ÖrdTiit Örd, Tapio Lönnberg, Einari Aavik, Seppo Ylä-Herttuala, Minna U. Kaikkonen

Single-cell ATAC-Seq data from human atherosclerosis. The files contain cells from endarterectomy samples from three donors, yielding approximately 7000 cells total. snATAC-Seq libraries were generated using the 10x Genomics scATAC-Seq v1 kit. The files were produced by the cellranger-atac v1.1 pipeline commands 'count' and 'aggr' (without normalization). The genome reference used was hg19 Reference v1.1.0.

Journal publication

Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

Tiit Örd, Kadri Õunap, Lindsey Stolze, Rédouane Aherrahrou, Valtteri Nurminen, Ilakya Selvarajan, Anu Toropainen, Tapio Lönnberg, Einari Aavik, Seppo Yla-Herttuala, Mete Civelek, Casey E Romanoski, and Minna U Kaikkonen

Circulation Research,

Files available

The file formats are described in detail at

1) cloupe-manual_cell_type_added.cloupe:
Loupe browser file for interactive browsing of the data. Includes a manual cell annotation into five principal cell lineages (smooth muscle cells, endothelial cells, macrophages, T/NK cells, and B/Plasma cells. For an overview of the Loupe Cell Browser ATAC software, please see

2) fragments.tsv.gz and fragments.tsv.gz.tbi:
Fragments file and the corresponding index file. Contains ATAC fragment locations (cut sites) from the hg19 genome and the cell barcode associated with the fragment. Used for displaying coverage of cuts in genomic regions, and could be used for recalling of peaks. For full information of the table structure, please see

3) matrix.mtx, peaks.bed and barcodes.tsv:
the peak-barcode matrix for cell-associated barcodes (contents of the "filtered_peak_bc_matrix" folder from cellranger-atac). Suitable for downstream analysis. For a full description of the matrix structure, please see

4) peak_annotation.tsv:
annotations for the peaks called by cellranger-atac. For a description of how peaks were annotated to genes, please see