Annotated clusters of cells from mouse brain with Alzheimer disease (from Nemri et al)

Seurat objects containing all brain cells (mouse_brain_after_clustering.rds) and selected clusters consisting of astrocytes and microglia (mouse_brain_after_2nd_clustering.rds). Single-cell transcriptomics data were obtained from the 10X Genomics website (https://www.10xgenomics.com/datasets/xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard). We derived the cell locations, types and sub-types from the spatial omics data, following standard single-cell transcriptomics methods in Seurat. Briefly, we performed a first round of SCTransform, RunPCA (npcs=30), RunUMAP, FindNeighbors, FindClusters (resolution 0.3) on the 60,829 cells. This resulted in 22 clusters, which we annotated manually using marker genes (using FindAllMarkers) (“mouse_brain_after_clustering.rds", 10.5281/zenodo.15966249). We then extracted the cells in the clusters 1 and 4, consisting primarily of astrocytes and microglia, to perform another round of clustering using SCTransform, RunPCA (npcs=30), RunUMAP, FindNeighbors, FindCLusters (resolution=1). Among the resulting 17 clusters, 14 clusters consisting of astrocytes sub-types and microglia sub-types were selected for downstream analysis (10,343 cells; Fig. S2). The remaining 3 clusters consisted of carry-over neurons and were removed from downstream analysis.