RNA-Seq enables the generation of extensive transcriptome information providing the capability to characterize transcripts (including alternative isoforms and polymorphism), to quantify expression and to identify differential regulation in a single experiment. Our aim in this study was to take advantage of using RNA-Seq high-throughput technology to provide a comprehensive transcriptome profiling of the sheep lactating mammary gland. Eight ewes of two dairy sheep breeds with differences in milk ...[more]
Project description:We have completed the high quality reference genome for domestic sheep (Oar v3.1). Early-stage Illumina GA sequence platform sequenced less reads in high GC content regions than in other regions. To read through higher GC content regions, we generated 2 Gb MeDIP-seq data for filling gaps in sheep reference genome assembly.
Project description:In the present study, we studied the effect of dietary selenium (Se) supplementation on the transcriptomic profile of sheep. The main objective was to evaluate the effect of Se-supplementation on the overall transcriptome of sheep, the altered pathways, and the biological processes related to it . A custom oligo microarray platform (AMADID: 070119) was designed, then used to profile gene expression from 20 samples from 10 sheep at two time points (T0; before Se-supplementation, and T40; at the end of a 40-d Se-supplementation period). Isolated and purified total RNAs were individually hybridized to the custom (4x44k) DNA microarray. The comparison of control and treated animal transcriptomes revealed a large set of differentially expressed genes. After functional analysis and qPCR validation, the result showed several pathways and biological processes that have been altered following Se-supplementation to the diet. Overall design: Ten lactating crossbred ewes (3 to 4 y of age and 55 to 65 kg BW) were assigned to a before-and-after experimental design, where each animal served as its own control. The sheep have been acclimatized (4-wk) on a basal diet containing a maintenance level of Se (0.13 mg Se/kg DM). At the end of the 4-wk acclimatization period the sheep started to receive the supra Se-supplemented diet (0.45 mg Se/kg DM) for a 40-d period. Blood samples were collected at 2 time points [T0; one day before the supra Se-supplementation, and T40; at the end of the 40-d supra Se-supplementation phase]. Blood samples were collected from each individual animal directly into Paxgene blood collection tubes, processed and stored at -20˚C till further analyses. All samples yielded high quality RNA that was tested prior the microarray setup.
Project description:Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 128 known miRNAs were identified, 526 novel miRNAs were predicted, and 202 differentially expressed miRNAs were found between the different tissues. Additionally, 4,422 candidate target genes were predicted, and 185 non-redundant GO annotation terms were identified using enrichment analysis. A total of 529 target genes were found to participate in 37 KEGG biological pathways, and 270 of these genes were significantly enriched in the metabolism category. Overall design: Examination of miRNA expression in 3 sheep intestinal regions.
Project description:Reproduction, as a physiologically complex process, can significantly affect the development of the sheep industry. However, a lack of overall understanding to sheep fecundity has long blocked the progress in sheep breeding and husbandry. Herein, in present study, we aimed to identify differentially expressed proteins (DEPs) from hypothalamus in sheep without FecB mutation in two comparison groups: polytocous (PF) versus (vs.) monotocous (MF) sheep at follicular phase and polytocous (PL) vs. monotocous (ML) sheep at luteal phase,expecting to provide an alternative method to identify DEPs associated with sheep prolificacy from the hypothalamus.
Project description:Comparison of genomic expression profiles in the mesenteric lymph nodes of naturally scrapie infected (clinical and preclinical stages) and control sheep. Expression profiles comparison of 7 clinical and 4 preclinical naturally scrapie infected sheep and 6 controls.