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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.
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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:

License:

Language:

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

Name:

Stockholm medicinska biobank

Type(s) of sample:

Patient breast tumor

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:

Sample size:

1

Source of the data:

  • Biological samples

Sample

Name:

breast tumor

Description of sample:

Tumor sample from one female breast cancer patient.

Instrument

Name:

Illumina Nextseq 550 or 2000 instrument

Type:

Technical instrument(s)

Description of the instrument:

Illumina sequencers

Geographic coverage

Geographic location:

Geographic description:

Patient is from Stockholm, Sweden.

Lowest geographic unit:

Region

Highest geographic unit:

Country

Administrative information

Responsible department/​unit:

Department of Oncology-Pathology [K7]

DOI:

10.17044/scilifelab.21378279.v1Opens in a new tab

Ethics Review:

Swedish Ethical Review Authority - 2016/957-31, 2017/742-32, 2021-00795, 2023-03734-02, 2025-03711-02.

Topic and keywords

CESSDA Topic Classification:

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Relations

Is supplemented by:

Developing mouse embryoOpens in a new tab

Is supplemented by:

Code for the analysis of spatial ATAC-seq dataOpens in a new tab

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).

Contact

Johan Hartmanjohan.hartman@ki.seOpens in a new tab

Metadata

Version 1
doris
ki
Published:|Updated: