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

posted on 01.11.2022, 13:33 authored by Margherita ZamboniMargherita Zamboni, Enric Llorens Bobadilla, Xinsong Chen, Johan Hartman

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


Vetenskapsrådet (Swedish Research Council)

Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)

Svenska Sällskapet för Medicinsk Forskning (Swedish Society for Medical Research)

Torsten Söderbergs Stiftelse (Torsten Söderberg Foundation)



Karolinska Institutet

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