Single-nuclei ATAC-Seq data from human atherosclerosis

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 by cellranger-atac v1.1 pipeline 'count' and 'aggr' (without normalization). The genome reference used was hg19 Reference v1.1.0. <br><br>The file formats are described in detail at https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/overview<br><br>Files available:<br>1) cloupe-manual_cell_type_added.cloupe: <br>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 https://support.10xgenomics.com/single-cell-atac/software/visualization/latest/what-is-loupe-cell-browser<br><br>2) fragments.tsv.gz and fragments.tsv.gz.tbi: <br>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 https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/fragments<br><br>3) matrix.mtx, peaks.bed and barcodes.tsv: <br>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 https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/matrices<br><br>4) peak_annotation.tsv: <br>annotations for the peaks called by cellranger-atac. For a description of how peaks were annotated to genes, please see https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/annotation<br><br><br>

本数据集为人类动脉粥样硬化的单细胞ATAC测序（single-cell ATAC-Seq）数据。数据来源于3名供体的动脉内膜切除术样本，总计获得约7000个细胞。本数据集的snATAC-Seq（single-nucleus ATAC-Seq）文库采用10x Genomics scATAC-Seq v1试剂盒构建。测序数据文件通过cellranger-atac v1.1版本的'count'与'aggr'流程生成（未进行标准化处理）。本次分析使用的基因组参考序列为hg19 Reference v1.1.0。

文件格式的详细说明可参见：https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/overview

可用文件如下：
1) cloupe-manual_cell_type_added.cloupe：用于该数据交互式浏览的Loupe浏览器文件。该文件包含手动注释的5种主要细胞谱系：平滑肌细胞、内皮细胞、巨噬细胞、T/NK细胞以及B/浆细胞。如需了解Loupe Cell Browser ATAC软件的详细信息，请访问：https://support.10xgenomics.com/single-cell-atac/software/visualization/latest/what-is-loupe-cell-browser

2) fragments.tsv.gz 及 fragments.tsv.gz.tbi：ATAC片段文件与对应的索引文件。该文件包含hg19基因组上的ATAC片段切割位点信息，以及与该片段关联的细胞条形码（cell barcode）。可用于展示基因组区域的切割覆盖度，也可用于峰的召回分析。如需了解该表格结构的完整说明，请访问：https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/fragments

3) matrix.mtx、peaks.bed 及 barcodes.tsv：细胞关联条形码的峰-条形码矩阵（对应cellranger-atac生成的filtered_peak_bc_matrix文件夹内容），适用于后续分析。如需了解该矩阵结构的完整说明，请访问：https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/matrices

4) peak_annotation.tsv：cellranger-atac所识别峰的注释文件。如需了解峰基因注释的具体方法，请访问：https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.1/output/annotation