Fig. 5: snCED-seq distinguishes major cell types and shows disease-cells in the 5XFAD brains.

a Overview of the experimental strategy. Created in BioRender. Tu, D. (2025) https://BioRender.com/hrx13a. b Cell map of mouse hippocampus in WT and AD by supervised clustering with ref. ²⁵. UMAP of 62,000 single-nucleus RNA profiles from hippocampi of Then, Nuclei were collected and resuspended 5-month-old male mice, three WT and three 5 × FAD (AD); colored by cluster. c Heat map showing expression of specific markers in all cell types, identifying each cluster in B. Expression level (color scale) of marker genes across clusters and the percentage of cells expressing them (dot size). d The frequency of each cluster in every sample. e The percentage of cell types in AD and WT. AD1 sample was screened. Data in the box plot correspond to the first (lower hinges) quartiles, third quartiles (upper hinges), and median (center). The upper whisker extends from the hinge to the maxima no further than 1.5 * IQR from the hinge. The lower whisker extends from the hinge to the minima at most 1.5 * IQR of the hinge. f DEG counts for each cell type The intensity of the blue colour was proportional to entry values. g The odds ratios of DEGs and AD-disease genes in every cluster. The dot size expresses cells association with the AD disease. Empty dot indicated statistical significance and crossed dot indicated non-significance (fisher’s exact test). and the specific p values are in the source data. n = 3 biological duplication, and bars show mean ± SD (e). Source data are provided as a Source Data file (b–g).