Mining sequencing and microarray data to study the transcriptome

Abstract

In the last decades, diverse techniques have emerged to study the transcriptome, i.e. the full range of messenger RNA, or mRNA, molecules expressed by an organism. High throughput sequencing and microarray techniques have highlighted the transcriptome complexity, including alternative splicing, non-coding RNAs, microRNAs among others. This thesis aims at studying transcriptional changes involved during Xenopus tropicalis metamorphosis, a model organism for developmental studies. The first chapter presents an overview of the most commonly used transcriptomics techniques, namely sequencing and microarrays. The second chapter describes a Sanger sequencing approach (ESTs) to characterize genes involved in metamorphosis. The third chapter describes the use of microarrays to study different time points during Xenopus metamorphosis. The fourth chapter presents different experimental settings on two-color microarrays and how to reconstruct time expression profiles from the raw data. The last chapter presents a review on gene expression profiling and data integration.