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2nd Global Summit on Plant Science

London, UK

Caroline Janitz

Caroline Janitz

Western Sydney University, Australia

Title: The influence of genomic contamination on the performance of illumina strand-specific RNA-Seq

Biography

Biography: Caroline Janitz

Abstract

The strand-specific RNA-Seq has been broadly utilized for comprehensive transcriptome surveys, including transcripts orientation and information, which is inaccessible when using conventional RNA-Seq. To retain the strand-specificity, it is highly recommended to remove genomic DNA from the RNA template. Despite current availability of improved DNase treatment protocols, removal of genomic DNA remains a technical challenge. This step in sample preparation is particularly difficult when dealing with samples with extremely low RNA concentrations. Moreover, DNase digestion demands additional purification step, which leads to loss of up to 30% of RNA template. Therefore a question arises whether an additional step of genomic DNA removal is essential. In order to address the impact of genomic DNA contamination on strand-specificity resolution, we used a tobacco model N. benthamiana that was depleted in ribonuclease J and essential for chloroplast RNA surveillance. Depletion of this RNase J results in massive accumulation of chloroplast antisense RNA. In this talk, I am going to present results of our analysis of changes in expression levels of reference sense and anti-sense transcripts in relation to degree of the RNA sample contamination with genomic DNA.