Spatially-resolved chromatin accessibility and transcriptomic profiling of human breast cancer

Human breast cancer OMICs data generated for the publication "Solid phase capture and profiling of open chromatin by spatial ATAC"

Abstract from the publication:

Current methods for epigenomic profiling are limited in the ability to obtain genome wide information with spatial resolution. Here we introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.

Dataset description

The dataset includes spatially-resolved chromatin accessibility profiling performed on three fresh-frozen tissue sections of HER2+ breast cancer. We provide raw data in the form of fastq files, along with processed feature barcode matrices, metadata, and photomicrographs of the tissue slices. Additionally the dataset contains spatially-resolved gene expression profiling of tissue sections from the same specimen. For this too, we provide raw and processed data, along with the metadata information.

Spatial transcriptomics data were generated using 10X Genomics' Visium platform, while spatial ATAC data were created using a method introduced in our publication, which relies on an analogous workflow. Samples were sequenced on Illumina Nextseq 550 or 2000 and raw data were processed with CellRanger Gene Expression or ATAC-seq pipelines.

To apply for conditional access to the dataset, please contact [e-mail] (mailto:[e-mail]) .

本数据集为发表于论文《固相捕获与空间ATAC（spatial ATAC）技术分析开放染色质（open chromatin）》所生成的人类乳腺癌组学（OMICs）数据。
该论文的摘要如下：
当前表观基因组分析（epigenomic profiling）方法在获取具备空间分辨率的全基因组信息方面能力有限。本研究提出空间ATAC（spatial ATAC）技术：该方法将组织切片中转座酶可及染色质（transposase-accessible chromatin）分析与条形码固相捕获（barcoded solid-phase capture）技术相结合，以实现空间分辨表观基因组学（spatially resolved epigenomics）研究。我们证实，空间ATAC技术可用于揭示小鼠器官发生、谱系分化以及人类病理过程中空间基因表达背后的调控程序。
数据集详情如下：
本数据集包含针对3例HER2阳性乳腺癌新鲜冷冻组织切片的空间分辨染色质可及性（chromatin accessibility）分析数据。我们提供fastq格式的原始数据，同时附带经过处理的特征条形码矩阵、元数据（metadata）以及组织切片的显微照片。
此外，本数据集还包含来自同一标本的组织切片空间分辨基因表达分析（gene expression profiling）数据，同样附带原始与处理后的数据及元数据。
空间转录组学（spatial transcriptomics）数据通过10X Genomics公司的Visium平台生成，而空间ATAC数据则采用本研究论文中介绍的方法构建，二者依赖相似的实验流程。
样本在Illumina Nextseq 550或2000测序仪上完成测序，原始数据通过CellRanger基因表达或ATAC-seq分析流程进行处理。
若申请该数据集的受控访问权限，请发送邮件至[e-mail]（mailto:[e-mail]）。