Fig. 3: Heterogeneity of immune cells across cattle tissues.
a, Bar chart displaying the number and proportion of 29 immune cell types in 58 tissues. The scatter plot represents the Shannon entropy values of immune cells in each tissue, with higher values indicating higher diversity. b, Heatmap showing the Pearson correlation of gene expression levels for each immune cell type, calculated based on the top 1,000 genes with the largest s.d. c, t-distributed stochastic neighbor embedding (t-SNE) visualization of annotated cell subtypes of myeloid cells, with cells color-coded according to subtype. d, Heatmap highlighting the average regulatory activity z-score of key TFs in 247 TFs that regulate the differentiation and maintenance of APC subtypes. e, Pseudotime trajectory analysis of monocyte and macrophage subtypes, with cell states colored on the trajectory tree. f, Statistical analysis of monocyte and macrophage subtype composition in each state. g, Heatmap showing the changes in gene expression of representative DEGs (q < 1 × 10−4) in pseudotime series, and GO enrichment analysis of DEGs reclustered into four clusters (bottom left). h, Representative pseudotime trajectory of marker genes in microglia across different states.
