Extended Data Fig. 10: Quality control of the human brain dataset and conserved gene expression changes across mouse AD models and human AD samples from the prefrontal cortex. | Nature Genetics

Extended Data Fig. 10: Quality control of the human brain dataset and conserved gene expression changes across mouse AD models and human AD samples from the prefrontal cortex.

From: A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains

Extended Data Fig. 10

a. Scatter plot showing the number of single-cell transcriptomes profiled in each human sample in two regions, colored by sexes. b. Box plots showing the number of unique transcripts (left) and genes (right) detected per nucleus profiled in the human dataset (Control SMTG: n = 36,781 cells, Control HIP (hippocampus): n = 30,801 cells; AD SMTG: n = 17,864 cells, AD HIP: n = 32,794 cells). c. Dotplot showing the markers for the main cell types identified in the human dataset. d-e. UMAP plot showing the integration between human and mouse cells, colored by the dataset (d) and main cell types (e). AS, astrocytes; BG, Bergmann glia; CGN, cerebellum granule neurons; CIntN, cerebellum interneurons; CPEC, choroid plexus epithelial cells; CPN 1, cortical projection neurons 1; CPN 2, cortical projection neurons 2; CPN 3, cortical projection neurons 3; DGN, dentate gyrus neurons; EC, endothelial cells; EpC, ependymal cells; HN, habenula neurons; HBN 1, hindbrain neurons 1; HBN 2, hindbrain neurons 2; IONN, Inferior olivary nucleus neurons; IMN 1, interbrain and midbrain neurons 1; IMN 2, interbrain and midbrain neurons 2; IntN1, interneurons 1; IntN2, interneurons 2; MG, microglia; OBN 1, OB neurons 1; OBN 2, OB neurons 2; OBN 3, OB neurons 3; OPC, oligodendrocyte progenitor cells; OLG, oligodendrocytes; PC, pituitary cells; PN, purkinje cells; SN 1, striatal neurons 1; SN 2, striatal neurons 2; UBC, unipolar brush cells; VLC, vascular leptomeningeal cells. f. Volcano plots showing AD-associated gene expression changes from human prefrontal cortex samples6 colored by main cell types. These genes show consistent changes in multiple cell subclusters between mouse AD models, human hippocampus and SMTG samples, and human prefrontal cortex samples from the above-mentioned publication. ASC, astrocytes; EX, excitatory neurons; INH, inhibitory neurons; MG, microglia; ODG, oligodendrocytes; OPC, oligodendrocyte progenitor cells; PER.END, pericyte/endothelial cells.

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