Comparison of spatial transcriptomics technologies used for tumor cryosections
Authors/Creators
-
Rademacher, Anne
(Data collector)1
-
Huseynov, Alik
(Data collector)2
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Bortolomeazzi, Michele
(Data collector)2
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Wille, Sina Jasmin
(Project member)1
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Schumacher, Sabrina
(Project member)1
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Sant, Pooja
(Project member)2
- Keitel, Denise (Project member)2
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Okonechnikov, Konstantin
(Project member)3
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Ghasemi, David
(Project member)3
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Pajtler, Kristian
(Project member)3
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Mallm, Jan-Philipp
(Project leader)2
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Rippe, Karsten
(Project leader)1
- 1. German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
- 2. German Cancer Research Center (DKFZ) Heidelberg, Single Cell Open Lab, Heidelberg, Germany
- 3. Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
Description
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).
Files
readme.txt
Files
(7.9 GB)
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Additional details
Related works
- Is supplement to
- Publication: 10.1101/2024.04.03.586404 (DOI)