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000302142 245__ $$aComparison of spatial transcriptomics technologies using tumor cryosections.
000302142 260__ $$aLondon$$bBioMed Central$$c2025
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000302142 520__ $$aSpatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid development of spatial transcriptomics methods, each with unique characteristics, makes it challenging to select the most suitable technology for specific research objectives. Here, we compare four imaging-based approaches-RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium-alongside Visium, a sequencing-based method. These technologies were employed to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features.Our analysis reveals that automated imaging-based spatial transcriptomics methods are well-suited to delineate the intricate MBEN microanatomy and capture cell-type-specific transcriptome profiles. We devise approaches to compare the sensitivity and specificity of different methods, along with their unique attributes, to guide method selection based on the research objective. Furthermore, we demonstrate how reimaging slides after the spatial transcriptomics analysis can significantly improve cell segmentation accuracy and integrate additional transcript and protein readouts, expanding the analytical possibilities and depth of insight.This study underscores important distinctions between spatial transcriptomics technologies and offers a framework for evaluating their performance. Our findings support informed decisions regarding methods and outline strategies to improve the resolution and scope of spatial transcriptomic analyses, ultimately advancing spatial transcriptomics applications in solid tumor research.
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000302142 650_7 $$2Other$$aMERFISH
000302142 650_7 $$2Other$$aMedulloblastoma
000302142 650_7 $$2Other$$aMerscope
000302142 650_7 $$2Other$$aMolecular Cartography
000302142 650_7 $$2Other$$aRNAscope
000302142 650_7 $$2Other$$aSpatial transcriptomics
000302142 650_7 $$2Other$$aVisium
000302142 650_7 $$2Other$$aXenium
000302142 7001_ $$0P:(DE-He78)c9e7edca388fdbfc1ea3c679db3143a6$$aHuseynov, Alik$$b1$$eFirst author$$udkfz
000302142 7001_ $$0P:(DE-He78)042bf671f0e43607f9c16be966711f16$$aBortolomeazzi, Michele$$b2$$eFirst author$$udkfz
000302142 7001_ $$0P:(DE-He78)5379d82331e87ab7e477ce09f4057b42$$aWille, Sina Jasmin$$b3$$udkfz
000302142 7001_ $$0P:(DE-He78)d70ddd73ff941566d830600443d2e69c$$aSchumacher, Sabrina$$b4$$udkfz
000302142 7001_ $$0P:(DE-He78)0178c28b2dee9e8a977975ba9ff006e2$$aSant, Pooja$$b5$$udkfz
000302142 7001_ $$0P:(DE-He78)03220ae5549c855f084614d817da3cc7$$aKeitel, Denise$$b6$$udkfz
000302142 7001_ $$0P:(DE-He78)34b3639de467b2c700920d7cbc3d2110$$aOkonechnikov, Konstantin$$b7$$udkfz
000302142 7001_ $$0P:(DE-HGF)0$$aGhasemi, David R$$b8
000302142 7001_ $$0P:(DE-He78)a7c1bbac024fa232d9c6b78443328d9d$$aPajtler, Kristian W$$b9$$udkfz
000302142 7001_ $$0P:(DE-He78)697cb039ca08f3b7e5a2a52dbf020b46$$aMallm, Jan-Philipp$$b10$$udkfz
000302142 7001_ $$0P:(DE-He78)94de5f7413279464b6e738d91dfae1eb$$aRippe, Karsten$$b11$$eLast author$$udkfz
000302142 773__ $$0PERI:(DE-600)2040529-7$$a10.1186/s13059-025-03624-4$$gVol. 26, no. 1, p. 176$$n1$$p176$$tGenome biology$$v26$$x1465-6906$$y2025
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