Preprocessed h5ad files of Xenium spatial transcriptomics performed on atherosclerotic human carotid artery samples

Xenium runs were performed with two panels of genes. The panels consist of a core list present in both panels (comprising 111 central genes for cell type annotations and key processes) as well as individual genes for the panels, resulting in a cell-defining (panel 1) and disease associated (panel 2) panel. In total 548 unique genes have been sequenced with both panels. Sequencing with panel 1 and panel 2 genes was performed on consecutive FFPE sections for each sample, thereby introducing a 5 µm shift in the morphology of the mounted Xenium slides across the panels. Detailed description of preprocessing steps can be found in our manuscript.