Comparison of spatial transcriptomics technologies used for tumor cryosections
DOI10.5281/zenodo.10863259Zenodo10863259MaRDI QIDQ6691763FDOQ6691763
Dataset published at Zenodo repository.
Sabrina Schumacher, Anne Rademacher, Kristian Pajtler, Karsten Rippe, Pooja Sant, Jan-Philipp Mallm, Sina Jasmin Wille, Konstantin Okonechnikov, David Ghasemi, Alik Huseynov, Denise Keitel, Michele Bortolomeazzi
Publication date: 2 April 2024
Copyright license: Creative Commons Attribution 4.0 International
This repository contains data from a spatial transcriptomics (ST) analysis of brain tumor cryosections (medulloblastoma with extensive nodularity, MBEN). It is associated with the preprint by Rademacher, Huseynov, Bortolomeazzi et al. 2024, bioRxiv, https://doi.org/10.1101/2024.04.03.586404, that has a full description of the work. In the study four imaging-based ST methods RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium as well as sequencing-based ST (Visium) and single cell RNA sequencing of dissociated nuclei (snRNA-seq) were compared. The files provided here are described in readme.txt and include the transcript count matrices acquired on the Visium platform as well as Seurat objects of the data and analysis results for the comparison of the different technologies. The data for snRNA-seq, RNAscope HiPlex and Molecular Cartography included in the Seurat objects are based on the primary data acquired in a previous study (Ghasemi et al. 2024, Nat Commun, https://doi.org/10.1038/s41467-023-44117-x).
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