Spatial Transcriptomics Data for jazzPanda

This repository contains spatial transcriptomics datasets used in the jazzPanda study, including raw, vendor-distributed data files and processed data objects (e.g. Seurat and SpatialExperiment objects) generated to support the jazzPanda paper and its associated analyses. This record serves as an archival mirror of publicly available raw data to support transparency and reproducibility; all downstream analyses and results are described in the jazzPanda paper and implemented in the accompanying analysis repository (https://github.com/phipsonlab/jazzPanda_paper).

The included datasets originate from multiple commercial platforms, including 10x Genomics Xenium, NanoString CosMx, and Vizgen MERSCOPE, and encompass mouse brain as well as multiple human cancer and healthy tissue samples. The data were accessed from the respective vendor portals in early 2025.

Public data sources:

1) 10x Xenium Mouse brain data: https://www.10xgenomics.com/resources/datasets/fresh-frozen-mouse-brain-replicates-1-standard

2) 10x Xenium Human HER2+ breast cancer data: https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast

3) 10x Xenium Human lung cancer data: https://www.10xgenomics.com/resources/datasets/xenium-human-lung-preview-data-1-standard

4) Nanostring CosMx Human liver healthy and cancer data: https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/human-liver-rna-ffpe-dataset/

5) Vizgen MERSCOPE Human breast cancer data: https://info.vizgen.com/ffpe-showcase?submissionGuid=c9a25730-3fe5-444b-bef8-1a74d51ddefb

Data reuse is subject to the original licensing and usage terms of the respective data providers.