2026-10-12 https://api.researchdata.se/oai-pmh

oai:researchdata.se:2025-265/1 2026-03-05 subject:ssif:106 subject:ssif:10609 subject:ssif:10614 subject:ssif:30108 subject:ssif:30113 subject:ssif:1 subject:ssif:301 subject:ssif:3 principal:slug:karolinska-institutet

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.48723/e39v-h234 Data for Solid phase capture and profiling of open chromatin by spatial ATAC Data för Solid phase capture and profiling of open chromatin by spatial ATAC https://orcid.org/0000-0002-7891-1272 https://orcid.org/0000-0003-0664-4707 https://orcid.org/0000-0002-3214-9075 https://orcid.org/0000-0002-6500-8527 SCIENCE AND TECHNOLOGY VETENSKAP OCH TEKNOLOGI Biotechnology Bioteknik Biological Sciences Biologi Genetics and Genomics Genetik och genomik Developmental Biology Utvecklingsbiologi Cell and Molecular Biology Cell- och molekylärbiologi Medical Bioinformatics and Systems Biology Medicinsk bioinformatik och systembiologi 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 Cell Ranger Gene Expression or ATAC-seq pipelines. info:eu-repo/semantics/restrictedAccess SE http://sws.geonames.org/2673722 https://creativecommons.org/licenses/by/4.0/ Karolinska Institutet Karolinska Institutet 2025-10-15T07:36:59.759456Z eng