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
Project description:Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual.
2018-12-05 | GSE123327 | GEO
Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0).
2013-08-09 | GSE41488 | GEO
Project description:Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2) 9 Chinese indigenous pig, one Chinese wild boar and 2 commercial pigs were detected using one pig of Duroc as reference. These 12 animals include 1 wild pig, 2 pigs each from Yorkshire and Landrace as the representatives of modern commercial breeds and 9 unrelated individuals selected from 6 Chinese indigenous breeds (2- Tibetan pig, 2- Diannan small-ear pig, 2-Meishan pig, 1- Min pig, 1-Daweizi pig, and 1-Rongchang pig).
2015-06-29 | E-GEOD-49299 | biostudies-arrayexpress
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs. To compare SNPs identified by genotyping arrays and de novo assembly method, we genotyped 10 pig breeds by porcine 60K BeadChip genotyping array (Illumina), including 1 berkshire pig, 1 hampshire pig, 1 landrace pig, 1 large white pig,1 piétrain pig, 1 bamei pig,1 jinhua pig, 1 meishan pig, 1 rongchang pig and 1 Tibetan wild boar.
2016-07-05 | E-GEOD-83910 | biostudies-arrayexpress
Project description:To study the development of pig facial skin after birth, we use the facial skin tissues of healthy Chenghua sows as experimental materials. we then performed gene expression profiling analysis using data obtained from RNA-seq of pig facial skin tissues at four time points.
2023-05-10 | GSE231573 | GEO
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.
2012-05-16 | GSE30334 | GEO