Project description:We report the application of next generation sequencing for examining muscle development in two different breeds of pigs (Hampshire and Mali). Muscle samples (n=2/breed) were subjected to RNA isolation, cDNA library preparation and sequencing.The transcriptome analysis shows significant differences in the expression pattern of genes associated with muscle development in Hampshire and Mali.
Project description:We report the application of methylated DNA immunopreciptation (MeDIP)-next generation sequencing for examining methylome in two different breeds of pigs. Two muscle samples from each animal/breed processed to isolated DNA. DNA was isolated from two muscle samples (one per breed) was used for methylated DNA immunoprecipitation (MeDIP). 5 methyl cytosine regions were immunoprecipitated and processed for next generation sequencing in Hiseq 2500 (Illumina). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment (BWA) (version 0.7.17). The MeDIP data generated was used for identification of differentially methylated regions (DMRs) across the chromosome between the breeds using Burrrows Eheeler Alignment (BWA version 0.7.17. Uniquely mapped reads were processed further with MEDIPS. A total of 1545 and 25 DMRs (P<0.1) were identified across the pig chromosome and mitochondrial DNA respectively.
