Extended Data Fig. 4: Preparation of the datasets for analysis and cell type/state annotations. | Nature Neuroscience

Extended Data Fig. 4: Preparation of the datasets for analysis and cell type/state annotations.

From: The Alzheimer’s therapeutic Lecanemab attenuates Aβ pathology by inducing an amyloid-clearing program in microglia

Extended Data Fig. 4: Preparation of the datasets for analysis and cell type/state annotations.The alternative text for this image may have been generated using AI.

a,b, Overview of the cDNA libraries used in scRNA-seq experiments (GAL002, GAL004, GAL005, H1 and H2), including the number of cells per sample (a) and the distribution of cells on the UMAP across different libraries after data integration (b). c, The UMAP plot of the 22,841 single xenografted human cells that passed quality control colored by clusters. d, UMAP plot colored by the expression level of MRC1, a macrophage marker. Notably, cluster 10, identified as the macrophage cluster, was removed from further analysis. e, Reactome pathway enrichment terms for significantly downregulated (black) and upregulated genes (red) ranked by p-value upon Lecanemab treatment (*: p.adj < 0.05, **: p.adj < 0.01, ***: p.adj < 0.001). Two-sided p-values were adjusted using the Benjamini–Hochberg (BH) correction. f, Top six most differentially expressed genes in each cell state. The dot size represents the percentage of cells within the given cluster expressing the gene. The dot color represents the scaled and normalized average expression of the gene. g, UMAP plots colored by the level of expression of FCGRs (encoding FcγRs) expressed by human microglia.

Back to article page