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

Xenium_final_dataset.zipXenium 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. Description of .obs columns is provided in the Xenium_column_descriptions.md file. Subregion_coordinates.zipThe annotation of sample subregions is a histological analysis, using established Oxford Plaque Studies and AHA criteria and was performed by an experienced cardiovascular pathologist. The borders of the annotated subregions were initially determined on the HE stained slides by a pathology expert, then transferred to the DAPI-stained slides manually by drawing the determined subregion borders by hand in Xenium Explorer. Individual subregion coordinates are contained in the .zip file. subregion_area_dict.pickleBorder coordinates were extracted from Xenium Explorer and converted to polygons, which then were used to assign individual cells to their respective subregions and to calculate the subregion areas. Subregion polygons and areas of individual samples, along with whole sample areas are contained in subregion_area_dict.pickle, in a Python pickled dictionary format. Detailed description of preprocessing steps can be found in our manuscript.