Fig. 5

Widespread activation of immune function and their associated gene expression in different cell types in four stomachs. A t-SNE maps of the cells in rumen, reticulum, omasum, and abomasum (left to right). B Immune-associated pathway activities of each cell type in rumen, reticulum, omasum, and abomasum (left to right). C Dot plot showing the expression patterns of genes associated with the defense or response to microorganism in different cells in rumen (upper left), reticulum (upper right), omasum (lower left), and abomasum (lower right). The genes and their function were obtained from GO database, only genes that expressed in at least one cell type (Percent expressed > 0) were kept. The names of the GO terms were used as the summary of the function of these genes (①–⑦)