Data for Solid phase capture and profiling of open chromatin by spatial ATAC
https://doi.org/10.48723/e39v-h234
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.
Documentation files
Documentation files
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
Research principal:
Data contains personal data:
Yes
Type of personal data:
Breast cancer patient genomic sequencing data
Code key exists:
Yes
Sensitive personal data:
Yes
Citation:
Language:
Method and outcome
Method and outcome
Unit of analysis:
Population:
One female breast cancer patient.
Time method:
Study design:
- Preclinical study
Description of study design:
One breast cancer patient with a large, treatment-naive tumor was recruited to the study, signed informed consent that allowed us to perform molecular analysis of her tumor after its removal with surgery.
Sampling procedure:
Description of sampling:
Breast cancer tissues were obtained from the Department of Clinical Pathology and Cancer Diagnostics at Karolinska University Hospital, Stockholm, Sweden. Experimental procedures and protocols were approved by the regional ethics review board (Etikprövningsnämnden) in Stockholm, and informed consent was obtained from the participating patient.
The samples were obtained from a breast tumor removed from a patient with treatment-naive invasive ductal carcinoma. The tumor was divided into several regions and collected freshly by a pathologist, depending on the size of the tumor. From each region, tissue was isolated for direct embedding in optimal cutting temperature compound, followed by immediate freezing and storage at −80 °C until further analysis.
Data format/data structure:
Samples/material - Collected from scientific collection/biobank
Samples/material - Collected from scientific collection/biobank
Name:
Stockholm medicinska biobank
Type(s) of sample:
Patient breast tumor
Data collection - Experiment
Data collection - Experiment
Mode of collection:
Experiment
Description of the mode of collection:
Data was collected through lab experiments and sequencing approaches using the above-mentioned patient tumor material.
Time period(s) for data collection:
2022-03-27 - 2022-03-27
Data collector:
- Karolinska Institutet
Opens a new window at ror.org.
ROR
Sample size:
1
Source of the data:
- Biological samples
Sample
Sample
Name:
breast tumor
Description of sample:
Tumor sample from one female breast cancer patient.
Instrument
Instrument
Name:
Illumina Nextseq 550 or 2000 instrument
Type:
Technical instrument(s)
Description of the instrument:
Illumina sequencers
Geographic coverage
Geographic coverage
Geographic location:
Geographic description:
Patient is from Stockholm, Sweden.
Lowest geographic unit:
Region
Highest geographic unit:
Country
Administrative information
Administrative information
Responsible department/unit:
Department of Oncology-Pathology [K7]
Identifiers
Identifiers
Ethical Review
Ethical Review
Reviewer:
- Swedish Ethical Review Authority
components.catalogue.resource.content.administrativeInformation.ethicalReview.rorId.srText
ROR
Registration number:
2016/957-31, 2017/742-32, 2021-00795, 2023-03734-02, 2025-03711-02.
Topic and keywords
Topic and keywords
CESSDA topic classification:
Swedish Standard Classification of Research Subjects 2025:
Relations
Relations
Is supplemented by:
Is supplemented by:
Publications
Publications
Citation:
Llorens-Bobadilla, E., Zamboni, M., Marklund, M. et al. Solid-phase capture and profiling of open chromatin by spatial ATAC. Nat Biotechnol 41, 1085–1088 (2023).
