Figure 4
From: Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei
The pipeline for sRNA prediction, sRNA validation by transcriptome cross-referencing, sRNA-mRNA interaction analyses and sRNA conservation based on sequence and structure similarities. (A) The dataset for sRNAs was collected from Ooi et al.18 and by using a modified version of the method reported by Khoo et al.19; (B) RNA-seq data from B. pseudomallei grown in different culture media were processed for differential expression analysis; (C) These sRNAs then were cross-referenced with RNA-seq data to validate their expressions; (D) For sRNAs that were observed to have flanking genes with significant differential expression, the interaction between sRNA-mRNA were analyzed using copraRNA followed by conservation analysis based on both sequence and secondary-structural similarities.
