Project description:Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol. Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina protocol or HD protocol
Project description:Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol.
Project description:In the present study we tested the hypothesis that male and female rat livers respond differently to a change in nutrient availability or to insulin treatment. We compared hepatic gene expression, hepatic glycogen and glucose output, insulin sensitivity and amino acids, using healthy rats. Keywords: Hepatic gene expression, sex-differences Two-condition experiment. Biological replicates: 4 male rat livers from rats on a standard diet and 4 female rat livers from rats on a standard diet. One replicate per array.
Project description:The sRNA population (sequence identity and distribution of abundances) in O sativa was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)
Project description:Messenger RNA (mRNA) translation can lead to higher rates of mRNA decay, suggesting a role for the ribosome in mRNA destruction. Furthermore, features of an mRNA, such as codon identities, that are directly probed by the ribosome also correlate with mRNA decay rates. Specifically, many amino acids are encoded by synonymous codons, and some synonymous codons are decoded by more abundant tRNAs leading to more optimal translation and increased mRNA stability. In addition to different translation rates, the presence of individual codons can lead to higher or lower rates of amino acid misincorporation which could potentially lead to protein misfolding if an individual amino acid makes many critical contacts in a structure. Here, we directly test whether amino acid misincorporation affects mRNA stability, taking advantage of an aminoglycoside antibiotic (G418) which promotes higher error rates in the ribosome. We observe that G418 decreases firefly luciferase mRNA stability in an in vitro system, and we similarly observe that G418 reduces mRNA stability in mouse embryonic stem cells (mESCs). G418-sensitive mRNAs are enriched for suboptimal hydrophobic amino acid codons as well as other codons that are known to result in higher rates of amino acid misincorporation. Since protein folding is highly sensitive to the identity of hydrophobic amino acids, these results strongly suggest that defects in protein folding are linked to mRNA decay.
Project description:The sRNA population (sequence identity and distribution of abundances) in M truncatula was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)
Project description:The sRNA population (sequence identity and distribution of abundances) in S Lycopersicum was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)
Project description:The sRNA population (sequence identity and distribution of abundances) in S Lycopersicum was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)