Project description:In this study, we generated 47 RNA-seq data for 14 tissues in Holstein cattle. We analyzed the variations of gene expression among tissues.
Project description:In this study, we generated whole genome bisulfite sequencing data of 19 samples for 13 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues. In this study, we generated whole genome bisulfite sequencing data of 6 samples for 5 tissues in Hereford cattle. We analyzed the variations of DNA methylation among tissues.
Project description:In this study, we generated 94 RNA-seq data that were colloced from different tissues in Hereford cow (L1 Dominette 01449) and its relatives. By combining these RNA-seq data with our other data and published data, we uniformly assembled and analyzed a total of 723 transcriptomes from 91 tissues and cell types in cattle, to identify tissue-specific genes with the highest specific expression. We then detected the trait-relevant tissues and cell types, and improved genomic prediction for milk production traits.
Project description:Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. Here we present an initial effort of single-cell transcriptomic analyses of cattle ruminal epithelial cells during the rumen development. We obtained 5064 and 1372 cells from Holstein ruminal epithelial cells before and after weaning, respectively. We reported 6 cell types across their temporal and spatial distributions, which were partially correlated with rumen epithelium layer’s structures and functions. We also reported a distinct sets of cell markers for these cell types, for example, CRA1, HMMR, MKI67, and EZH2 for the dividing epithelial cells and the TGFB pathway and the keratin gene family for keratinized epithelial cells. Our proposed a cell lineage model may contribute to the understanding of cattle rumen epithelial proliferation and development.
Project description:In this study, we generated whole genome bisulfite sequencing data of 2 samples for Bones in Holstein cattle. We analyzed the variations of DNA methylation among tissues compared to other tissues we generated before.
Project description:Comprehensive analyses of tissues at the single-cell level will benefit our understanding of genetic bases for complex traits. We performed single-cell RNA sequencing (scRNA-seq) analyses of peripheral blood mononuclear cells (PBMCs) from Holstein cattle, investigating their cell types and responses to lipopolysaccharide (LPS) treatment in vitro. The responses to LPS treatment include innate immunity activation of monocytes, macrophages, and dendritic cells, as well as B cell proliferation. The innate immunity responses are featured with CCL2 and CXCL2 proinflammatory cytokines. We detected trait-relevant cell types and found that DEGs induced by LPS were significantly associated with many complex traits of economic value in Holstein.
