Project description:This SuperSeries is composed of the following subset Series: GSE42279: AAPH-treated blastocysts vs CTL-treated blastocysts GSE42280: BSO-treated blastocysts vs CTL-treated blastocysts Refer to individual Series
Project description:Comparison of the transcription (coding and lncRNAs) of in vitro cultured bovine SAM-treated blastocysts and non-treated blastocysts
Project description:EtOH-Lipid form serum have been added in BSA-supplemented SOF during post-compaction development of IVP bovine embryos. Lipid-treated blastocysts were compared with control treated blastocysts (no lipid addition to BSA, EtOH balanced). Amplified anti-sense RNA from each sample (4 pools of control and 4 pools of treated blastocysts) were labeled then hybridized on oligonucleotide microarrays following a dye-swap design (ex: pool 1 ctl in red vs. pool 1 treatment in green and then pool 1 ctl in green vs. pool 1 treatment in red).
Project description:The Toll-like receptor (TLR) and peptidoglycan recognition protein 1 (PGLYRP1) genes play key roles in the innate immune systems of mammals. While the TLRs recognize a variety of invading pathogens and induce innate immune responses, PGLYRP1 is directly microbicidal. We used custom allele-specific assays to genotype and validate 220 diallelic variants, including 54 nonsynonymous SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) for 37 cattle breeds. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and we were unable to differentiate between the specialized B. t. taurus beef and dairy breeds, despite an average polymorphism density of one locus per 219 bp. Ninety-nine tagSNPs and one tag insertion-deletion polymorphism were sufficient to predict 100% of the variation at all 11 innate immune loci in both subspecies and their hybrids, whereas 58 tagSNPs captured 100% of the variation at 172 loci in B. t. taurus. PolyPhen and SIFT analyses of nonsynonymous SNPs encoding amino acid replacements indicated that the majority of these substitutions were benign, but up to 31% were expected to potentially impact protein function. Several diversity-based tests provided support for strong purifying selection acting on TLR10 in B. t. taurus cattle. These results will broadly impact efforts related to bovine translational genomics.