Project description:Rumen epithelial parakeratosis, a common disease in ruminants caused by abnormalities in the ruminal stratified squamous epithelial keratinization process, negatively impacts ruminant health and performance. While we still lack a comprehensive perception of the underlying mechanisms and the predisposing factors for this disorder.Here, we investigated rumen epithelial cell heterogeneity, differentiation trajectories, and cornification to clarify the rumen epithelial keratinization process
Project description:To investigate the evolutionary changes of regulatory elements in ruminants, we then performed regulatory elements profiling analysis using ChIP-seq datasets (H3K27ac and H3K4me3) of liver from three ruminants.
Project description:To investigate the evolutionary changes of gene expression in ruminants, we performed gene expression profiling analysis using RNA-seq data of liver from three ruminants.
Project description:To describe the gene expression profile of brain and muscle across ruminants, we performed gene expression analysis of brain and muscle using RNA-seq data for three ruminants.
Project description:Newborn ruminants are considered as functionally monogastric animals. The poorly understanding of tremendous cellular differences between newborn and completely ruminating stages hinders the improvement of health and performance of domestic ruminants. Here, unbiased single-cell RNA sequencing was performed on the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, rectum, salivary gland, liver, and mammary gland from newborn and adult cattle. We created a comprehensive single-cell transcriptomic compendium covering 235,941 high-quality single cells and 78 cell types. The age-state cell atlases for each tissue type were also constructed to delineate the cell type composition dynamics at newborn and adult stages. We further created the Cattle Cell Landscape database (http://cattlecelllandscape.zju.edu.cn) to detailly display the informative results and to facilitate in effectively annotation of cattle cell type/subtypes for the broad research community. By measuring stemness states of epithelial cells across multiple tissue types, we revealed a multi-tissue representation of paradigm of cell stemness plasticity: the newborn forestomach (rumen, reticulum, and omasum) epithelial cells are more transcriptionally indistinct and stochastic compared with adult stage, which contrary to that of abomasum and intestinal tissues. Moreover, the rapid forestomach development during the early life of calves was driven by the epithelial progenitor-like cells with high activities of epigenetic modifying. A novel cell type STOML3+ cell was found to be newborn cattle-specific that plays an important role in stemness maintenance of its own and cholangiocyte in the hepatic microenvironment. These results provide novel insights into the cellular biology and postnatal ruminating maturity of ruminants
