Project description:This study aims to investigate the transcriptomic profile of the pig limbic and endocrine tissues, which are important in stress response and hence the pig’s health and welfare and production. We performed a total of 48 RNA-seq of the amygdala, hippocampus, thalamus, hypothalamus, pituitary gland, and adrenal gland obtained from 8 individual pigs. We identified differentially expressed genes across tissue-types, co-expressed gene modules and their associations with specific tissue types by Weighted Gene Co-expression Network Analysis (WGCNA) and allele-specific expression (ASE) within and between tissues.
Project description:This experiment investigated chromatin accessibility of the pig limbic and endocrine tissues, which are important in stress response and hence the pig’s health and welfare and production. We carried out a total of 48 ATAC-seq profiles of the amygdala, hippocampus, thalamus, hypothalamus, pituitary gland, and adrenal gland obtained from 8 individual pigs. We compared the chromatin accessibility landscape across tissue-type, annotated differentially accessible genomic regions and functionally mapped them.
Project description:Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues. Are all tissues equally affected by breed or sex? How relevant is tissue in terms of total transcriptome variability? Experiment Overall Design: In order to gain insight on these issues, we have microarrayed 16 different tissues hybridization on Affymetrix microarrays from four animals of the extreme pig breeds Large White and Iberian, two males and two females
Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context. Eleven small RNA libraries from eight adipose tissues, two skeletal muscle tissues and cardiac muscle of pig were sequenced.
Project description:To better understand the molecular mechanisms of right ventriuclar dysfunction in CTEPH pig model, a RNA sequencing analysis was performed in RV tissues collected from 5 CTEPH pigs and 5 sham opereted pigs.
Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context.
Project description:It is evident that epigenetic factors, especially DNA methylation, play essential roles in obesity development. To learn systematic association of DNA methylation to obesity, we used pig as a model, and sampled eight diverse adipose tissues and two distinct skeletal muscle tissues from three pig breeds with distinguished fat levels: the lean Landrace, the fatty Rongchang, and the feral Tibetan pig. We sequenced 180 methylated DNA immunoprecipitation (MeDIP) libraries, generated 1,381 Gbp sequence data, and provided a genome-wide DNA methylation map for pig adipose and muscle studies. The analysis showed global similarities and differences between breeds, genders and tissues, and identified the differentially methylated regions (DMRs) that are preferentially located in intermediate CpG promoters and CpG island shores. The DMRs in promoters are highly associated to obesity development. We also analyzed methylation and regulation of the known obesity-related genes and predicted novel candidate genes. The comprehensive map here provides a solid base for exploring epigenetic mechanisms of adipose deposition and muscle growth.
Project description:Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. These results highlight some possible candidate genes for porcine adipose deposition and muscle growth and provide some data on which to base further studies of the molecular basis of energy metabolism.