Bos taurus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA264403 | ENA |
REPOSITORIES: ENA
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Project description:Comparison of L-carnitine treated day 6 in vivo bovine embryos to controls, in both the Jersey and Holstein breeds.
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Project description:Some embryos display better survival potential to cryopreservation than others. The cause of such phenotype is still unclear and might be due to cell damage during cryopreservation, resulting from over-accumulation and composition of lipids. In cattle embryos, in vitro culture conditions have been shown to impact the number of lipid droplets within blastomeres. So far, the impact of breed on embryonic lipid content has not yet been studied. In this study were compared the colour, lipid droplet abundance, lipid composition, mitochondrial activity, and gene expression of in vivo collected Jersey breed embryos which are known to display poor performance post-freezing and in vivo Holstein embryos which have good cryotolerance. Holstein in vivo day 6 embryos vs Jersey in vivo day 6 embryos: 4 replicates of each breed, with dye-swap.
2014-10-22 | E-GEOD-62553 | biostudies-arrayexpress
Project description:Uterus epithelial cells collected from Holstein Friesian cows with or without embryos
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Project description:Characterisation of the whole blood mRNA transcriptome in Holstein-Friesian and Jersey calves in response to gradual weaning
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Project description:Gene expression analysis of bovine day 16 embryos obtained from SCNT and IVP pregnancies
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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.
| S-EPMC2806759 | biostudies-literature
Project description:BackgroundWe present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque.ResultsThe assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information.Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly.ConclusionThe biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research.
| S-EPMC2686734 | biostudies-literature
Project description:MicroRNA expression in bovine satellite cells at 6th day of in vitro differentiation - myotubes (Hereford & Limousin vs Holstein-Freisian cattle)
| PRJNA297871 | ENA