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
Protocol for high-resolution 3D spatial transcriptomics using Open-ST / Schott, Marie; León-Periñán, Daniel; Splendiani, Elena; Ferretti, Elisabetta; Macino, Giuseppe; Karaiskos, Nikos; Rajewsky, Nikolaus. - In: STAR PROTOCOLS. - ISSN 2666-1667. - 6:1(2025). [10.1016/j.xpro.2024.103521]
Protocol for high-resolution 3D spatial transcriptomics using Open-ST
Splendiani, Elena;Ferretti, Elisabetta;Macino, Giuseppe;Rajewsky, Nikolaus
2025
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.1I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
