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.
Project description:Whole RNA transcriptome was performed on bovine lung granulomatous tissues from Mycobacterium orygis infected cattle and compared with healthy cattle lung 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: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:Long-read Nanopore cDNA sequencing of polyA-enriched RNA was implemented in a range of adult tissues isolated from cattle, pig, and chicken. These data were used to identify and characterize the expression patterns of full-length transcript isoforms.
Project description:Cattle plays an important role in providing essential nutrients through meat production. Thus, we focused on epigenetic factors associated with meat yield. To investigating circulating miRNAs that are involved with meat yield and connect biofluids and longissimus dorsi (LD) muscle in Korean cattle, we performed analyses of the carcass characteristics, miRNA array, qPCR, and bioinformatics. Carcass characteristics relative to the yield grade (YG) showed that the yield index and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A (equal to high yield grade) cattle among the three YGs. miRNA array sorted the circulating miRNAs that connect biofluids and LD muscle. miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with biofluids and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting biofluids and LD muscle because the target genes of miR-26b was more involved with myogenesis. Then, miR-26b targeted genes, DIAPH3 and YOD1 were downregulated in YG A cattle. Our results suggest that miR-15a, miR-26b, and miR-29c are upregulated in biofluids and LD muscle whereas, downregulation of DIAPH3 and YOD1 in the LD muscle of finishing cattle steers.
