The analysis of transcriptome, which was over the past decade based mostly on microarray technologies, is now being superseded by so-called next generation sequencing (NGS) systems that changed the way to explore entire transcriptome. RNA sequencing (RNA-Seq), one application of NGS, is a powerful tool, providing information not only about the expression level of genes but also further about th...

Motivations RNA editing is a widespread molecular phenomenon which modifies primary transcripts at specific positions [1]. It occurs in a variety of organisms including human and cooperates with alternative splicing in increasing both proteomic and transcriptomic complexity. RNA Editing can modulate gene expression and affect protein functionality. In human, such phenomenon is highly frequent i...

The deep sequencing of an mRNA population, RNA-seq, is a very successful application of next-generation sequencing technologies (NGSTs). RNA-seq takes advantage of two key NGST features: (1) samples can be mixtures of different DNA pieces, and (2) sequencing provides both qualitative and quantitative information about each DNA piece analyzed. We recently used RNA-seq to study the transcriptome ...

RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using R...

MOTIVATION Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived. RESULTS...

Crohn disease (CD) is a type of inflammatory bowel that causes inflammation in the digestive tract. Cases CD are increasing worldwide, calling for more research to elucidate pathogenesis CD. For this purpose, usage RNA-sequencing (RNA-seq) technique increasingly appreciated, as it captures RNA expression patterns at particular time point high-throughput manner. Although many RNA-seq datasets ge...

Two commonly used laboratory strains of C. albicans (BWP17 and SN148) were cultured independently at 30°C for in rich medium and used to prepare RNA in all described sequencing experiments. RNA was prepared from mitochondria purified by differential centrifugation as described in Methods, treated with RNase-free DNAse, and the quality of each preparation was assessed by conventional agarose gel...

Here we outline a next-generation RNA sequencing protocol that enables de novo assemblies and intra-host variant calls of viral genomes collected from clinical and biological sources. The method is unbiased and universal; it uses random primers for cDNA synthesis and requires no prior knowledge of the viral sequence content. Before library construction, selective RNase H-based digestion is used...