Data för Solid phase capture and profiling of open chromatin by spatial ATAC Data for Solid phase capture and profiling of open chromatin by spatial ATAC 2025-265-1 https://doi.org/10.48723/e39v-h234 Swedish National Data Service Svensk nationell datatjänst Landing page Data för Solid phase capture and profiling of open chromatin by spatial ATAC Data for Solid phase capture and profiling of open chromatin by spatial ATAC 2025-265-1 https://doi.org/10.48723/e39v-h234 10.1038/s41587-022-01603-9 Llorens-Bobadilla, Enric Llorens-Bobadilla, Enric Zamboni, Margherita Zamboni, Margherita Chen, Xinsong Chen, Xinsong Hartman, Johan Hartman, Johan Swedish National Data Service Svensk nationell datatjänst Landing page BIOTECHNOLOGY BIOTEKNIK Genomics Genomik Epigenomics Epigenomik HEALTH-RELATED BIOTECHNOLOGY MEDICINSK BIOTEKNIK SCIENCE AND TECHNOLOGY VETENSKAP OCH TEKNOLOGI Biotechnology Bioteknik 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. 2022-03-27 2022-03-27 Sweden Sverige IndividualIndividual IndividIndivid One female breast cancer patient. One female breast cancer patient. Other OtherOther ÖvrigtÖvrigt 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.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. OtherOther ÖvrigtÖvrigt Data was collected through lab experiments and sequencing approaches using the above-mentioned patient tumor material.Data was collected through lab experiments and sequencing approaches using the above-mentioned patient tumor material. ExperimentExperiment ExperimentExperiment Access to data through SND. Access to data is restricted. Åtkomst till data via SND. Tillgång till data är begränsad. restrictedAccess 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). 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). 10.1038/s41587-022-01603-9 2023