Fig. 4: ssREAD facilitates comprehensive spatial transcriptomics analyses synergized with scRNA-seq datasets.
From: A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)
a UMAP representation of cell types derived from the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD). Clockwise from the top left, corner insets elucidate the Braak stage, Thal phase, ethnicity, and sex attributes. b–e Bar plots visualizing the distribution of cells based on the Braak stage, Thal phase, sex, and ethnicity, categorized by the condition in the atlas. f Bar plots displaying the fractional representation of cell types, contrasting AD and control within the SEA-AD atlas. g Heatmap of top and bottom 25 DEGs identified between AD and control samples in the integrated AD035 MTG dataset in Microglia. h Comparison of DEGs overlap in Microglia among AD035 MTG, AD048 PFC, and their integrated datasets. i–l Deconvolution analysis of cell types between ST samples (ST01101 and ST01103) and the scRNA-seq SEA-AD atlas, showing the cell type fractions for Astrocytes (j) and Oligodendrocytes (l). Marker gene expression indicators, GFAP for Astrocytes (i) and MOBP for Oligodendrocytes (k). m–t Spatial distributions of DEGs in AD and control samples within MAPLE cluster 1, cross-validated with single-cell DEGs from the integrated AD035 datasets. Upregulated DEGs in Astrocytes GJA1 (m) and MT-ATP8 (n). Downregulated DEGs in Astrocytes IFITM3 (q) and TUBB2B (r). Upregulated DEGs in Oligodendrocyte ERBIN (o), GPRC5B (p), MID1IP1 (s), and SLC44A1 (t).
