ssbd-repos-000425
Xenium data for a comparison of spatial transcriptomics technologies for medulloblastoma cryosections
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Title
Xenium data for a comparison of spatial transcriptomics technologies for medulloblastoma cryosections
Description
10X Genomics Xenium data from human Medulloblastoma samples. The data was acuired in the course of a study performing a comparison of four imaging-based ST methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium – together with sequencing-based ST (Visium). These technologies were used to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features. Our analysis reveals that automated imaging-based ST methods are well suited to delineating the intricate MBEN microanatomy, capturing cell-type-specific transcriptome profiles. We devise approaches to compare the sensitivity and specificity of the different methods together with their unique attributes to guide method selection based on the research aim. Furthermore, we demonstrate how reimaging of slides after the ST analysis can markedly improve cell segmentation accuracy and integrate additional transcript and protein readouts to expand the analytical possibilities and depth of insights. This study highlights key distinctions between various ST technologies and provides a set of parameters for evaluating their performance. Our findings aid in the informed choice of ST methods and delineate approaches for enhancing the resolution and breadth of spatial transcriptomic analyses, thereby contributing to advancing ST applications in solid tumor research.
Submission date
2025-03-07
Funding information
Deutsche Forschungsgemeinschaft: INST 35/1503-1 FUGG NFDI 46/1 – 501864659
Ministry of Science, Research and the Arts Baden-Württemberg: INST 35/1314-1
Bundesministerium für Bildung und Forschung: SATURN3 (01KD2206B)
File formats
csv, csv.gz (GZ), h5, html, json, ome.tif, parquet, zarr.zip (ZIP)
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80 files / 40.88 GiB
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4 files / 40.65 GiB
Persons
Name
Michele Bortolomeazi
Contact, Other, Other
Name
Anne Rademacher
Imaging contributor, Quantitative data contributor
Name
Alik Huseynov
Imaging contributor, Quantitative data contributor
Name
Sina J. Wille
Imaging contributor, Quantitative data contributor
Name
Sabrina Schumacher
Imaging contributor, Quantitative data contributor
Name
Pooja Sant
Imaging contributor, Quantitative data contributor
Name
Denise Keitel
Imaging contributor, Quantitative data contributor
Name
Konstantin Okonechnikov
Imaging contributor, Quantitative data contributor
Name
David R. Ghasemi
Imaging contributor, Quantitative data contributor
Name
Kristian W. Pajtler
Imaging contributor, Quantitative data contributor
Name
Jan-Philipp Mallm
Imaging contributor, Quantitative data contributor
Name
Karsten Rippe
Imaging contributor, Quantitative data contributor
Ontology terms
Medical subject heading
-
Biological imaging method
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