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

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Item Type:	Article
Title:	Protocol for high-resolution 3D spatial transcriptomics using Open-ST
Creators:	Schott, M. ORCID: https://orcid.org/0009-0000-7393-2421, León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Splendiani, E. ORCID: https://orcid.org/0000-0003-4259-9093, Ferretti, E., Macino, G., Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
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.
Keywords:	Gene Expression Profiling, Three-Dimensional Imaging, Transcriptome, Animals
Source:	STAR Protocols
ISSN:	2666-1667
Publisher:	Cell Press / Elsevier
Volume:	6
Number:	1
Page Range:	103521
Number of Pages:	1
Date:	21 March 2025
Official Publication:	https://doi.org/10.1016/j.xpro.2024.103521
PubMed:	View item in PubMed

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