Protocol for high-resolution 3D spatial transcriptomics using Open-ST

Marie Schott; Daniel León-Periñán; Elena Splendiani; Elisabetta Ferretti; Giuseppe Macino; Nikos Karaiskos; Nikolaus Rajewsky

doi:10.1016/j.xpro.2024.103521

Protocol for high-resolution 3D spatial transcriptomics using Open-ST

STAR Protoc. 2024 Dec 19;6(1):103521. doi: 10.1016/j.xpro.2024.103521. Online ahead of print.

Authors

Marie Schott¹, Daniel León-Periñán¹, Elena Splendiani², Elisabetta Ferretti³, Giuseppe Macino⁴, Nikos Karaiskos⁵, Nikolaus Rajewsky⁶

Affiliations

¹ Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany.
² Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany; Department of Experimental Medicine, Sapienza University, Rome, Italy.
³ Department of Experimental Medicine, Sapienza University, Rome, Italy.
⁴ Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany; Department of Cellular Biotechnologies and Hematology, La Sapienza University of Rome, 00161 Rome, Italy. Electronic address: macino@bce.uniroma1.it.
⁵ Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany. Electronic address: nikolaos.karaiskos@mdc-berlin.de.
⁶ Laboratory for Systems Biology of Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str. 28, 10115 Berlin, Germany; Charité - Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany; NeuroCure Cluster of Excellence, Berlin, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; National Center for Tumor Diseases (NCT), Site Berlin, Berlin, Germany. Electronic address: rajewsky@mdc-berlin.de.

PMID: 39708325
DOI: 10.1016/j.xpro.2024.103521

Abstract

Spatial transcriptomics (ST) is fundamental for understanding molecular mechanisms in health and disease. Here, we present a protocol for efficient and high-resolution ST in 2D/3D with Open-ST. We describe all steps for repurposing Illumina flow cells into spatially barcoded capture areas and preparing ST libraries from stained cryosections. We detail the computational workflow for generating 2D/3D molecular maps ("virtual tissue blocks"), aligned with histological data, unlocking molecular pathways in space. Open-ST is applicable to any tissue, including clinical samples. For complete details on the use and execution of this protocol, please refer to Schott et al.¹.

Keywords: RNA-seq; bioinformatics; cancer; microscopy; systems biology.