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Comparison of spatial transcriptomics technologies using tumor cryosections

Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid development of spatial transcriptomics methods, each with unique character...

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Main Authors: Rademacher, Anne (Author) , Huseynov, Alik (Author) , Bortolomeazzi, Michele (Author) , Wille, Sina Jasmin (Author) , Schumacher, Sabrina (Author) , Sant, Pooja (Author) , Keitel, Denise (Author) , Okonechnikov, Konstantin (Author) , Ghasemi, David R. (Author) , Pajtler, Kristian Wilfried (Author) , Mallm, Jan-Philipp (Author) , Rippe, Karsten (Author)
Format: Article (Journal)
Language:English
Published: December 2025
In: Genome biology
Year: 2025, Volume: 26, Issue: 1, Pages: 1-32
ISSN:1474-760X
DOI:10.1186/s13059-025-03624-4
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1186/s13059-025-03624-4
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Author Notes:Anne Rademacher, Alik Huseynov, Michele Bortolomeazzi, Sina Jasmin Wille, Sabrina Schumacher, Pooja Sant, Denise Keitel, Konstantin Okonechnikov, David R. Ghasemi, Kristian W. Pajtler, Jan-Philipp Mallm and Karsten Rippe
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Summary:Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid development of spatial transcriptomics methods, each with unique characteristics, makes it challenging to select the most suitable technology for specific research objectives. Here, we compare four imaging-based approaches - RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium - alongside Visium, a sequencing-based method. These technologies were employed to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features.
Item Description:Online erschienen: 20. Juni 2025
Gesehen am 08.12.2025
Physical Description:Online Resource
ISSN:1474-760X
DOI:10.1186/s13059-025-03624-4

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