Similar Datasets
Project description:The wide application of pig disease model has caused a surge of interest in the study of derivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to ribosome, chromatin remodeling, and genes involved in cell cycle that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naive pluripotency in pig cells.
2016-01-07 | E-MTAB-2643 | biostudies-arrayexpress
Project description:miRNA-seq data of pig alveolar macrophages from 4 pig breeds.
2022-08-28 | GSE143660 | GEO
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. 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 genome-wide DNA methylation differences among breeds, males and females, and tissues.
2012-05-16 | E-GEOD-30344 | biostudies-arrayexpress
Project description:Metagenomes of stool samples from 54 pig farmers, 24 broiler farmers and 70 slaughter line workers.
| EGAD00001005444 | EGA