Project description:Background: Previous studies comparing quantitative proteomics and microarray data have generally found poor correspondence between the two. We hypothesised that this might in part be because the different assays were targeting different parts of the expressed genome and might therefore be subjected to confounding effects from processes such as alternative splicing. Results: Using a genome database as a platform for integration, we combined quantitative protein mass spectrometry with Affymetrix Exon array data at the level of individual exons. We found significantly higher degrees of correlation than have been previously observed (r=0.808). The study was performed using cell lines in equilibrium in order to reduce a major potential source of biological variation, thus allowing the analysis to focus on the data integration methods in order to establish their performance. Conclusion: We conclude that much of the variation observed when integrating microarray and proteomics data may occur as a consequence both of the data analysis and of the high granularity to which studies have until recently been limited. The approach opens up the possibility for the first time of considering combined microarray and proteomics datasets at the level of individual exons and isoforms, important given the high proportion of alternative splicing observed in the human genome.
Project description:We used two novel, and previously optimized, analytical approaches, CITE-Seq and Quantitative Phopho-Proteomics, to perform detailed and cohesive characterization of the same paired PBMC and sera samples collected from patients at the acute and convalescent phases of infection with different microbial pathogens.
Project description:The transcriptome of the amphipod Echinogammarus marinus was sequenced after exposure to hypoxia following acclimation to different temperatures using 100BP paired-end Illumina HiSeq sequencing. Amphipods were acclimated to two temperatures, 10 or 20 °C, for one week before individuals were then acutely exposed to normoxic (80% air saturation) or hypoxic conditions (30% air saturation) at 10 °C (n = 5 per experimental treatment).
Project description:We report the effect of incubation temperature on embryos and larvae of Solea senegalensis subjected to two different incubation temperatures (15 °C or 21 °C). We found that at some stages, a higher incubation temperature was associated with the expression of miRNAs positively related with growth Examination of miRNA expression in Senegalese sole whole embryos and larvae subjected to two different incubation temperatures, using the SOLiD platform and validation by qPCR