Data for Solid phase capture and profiling of open chromatin by spatial ATAC
type: Dataset
distribution: Landing page for the dataset
title: Data för Solid phase capture and profiling of open chromatin by spatial ATAC @sv
description: 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.
modified: 2026-03-05T12:12:28.593046Z
issued: 2025-10-15T07:36:59.759456Z
publisher: Karolinska Institutet
theme: HEAL
access rights: NON PUBLIC
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Enric Llorens-Bobadilla
    type: Agent
    account: https://orcid.org/0000-0002-7891-1272
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Margherita Zamboni
    type: Agent
    account: https://orcid.org/0000-0003-0664-4707
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Xinsong Chen
    type: Agent
    account: https://orcid.org/0000-0002-3214-9075
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Johan Hartman
    type: Agent
    account: https://orcid.org/0000-0002-6500-8527
    type: PrivateIndividual(s)
contact point: Individual
  fn: Xinsong Chen
contact point: Individual
  fn: Johan Hartman
keyword: BIOTECHNOLOGY
keyword: BIOTEKNIK @sv
keyword: Genomics
keyword: Genomik @sv
keyword: Epigenomics
keyword: Epigenomik @sv
keyword: HEALTH-RELATED BIOTECHNOLOGY
keyword: MEDICINSK BIOTEKNIK @sv
language: ENG
spatial: Sweden
spatial: Stockholm County

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: Data for Solid phase capture and profiling of open chromatin by spatial ATAC
availability: stable

Karolinska Institutet
type: Agent
type: Academia-ScientificOrganisation
source: https://ror.org/056d84691

Sweden
type: Location
label: Sverige @sv

Stockholm County
type: Location
label: Stockholms län @sv