T-REx: Transcriptome analysis webserver for RNA-seq Expression data

Abstract

BackgroundTranscriptomics analyses of bacteria (and other organisms) provide global as well as detailed information on gene expression levels and, consequently, on other processes in the cell. RNA sequencing (RNA-seq) has over the past few years become the most accurate method for global transcriptome measurements and for the identification of novel RNAs. This development has been accompanied by advances in the bioinformatics methods, tools and software packages that deal with the analysis of the large data sets resulting from RNA-seq efforts.ResultsBased on years of experience in analyzing transcriptome data, we developed a user-friendly webserver that performs the statistical analysis on the gene expression values generated by RNA-seq. It also provides the user with a whole range of data plots. We benchmarked our RNA-seq pipeline, T-REx, using a case study of CodY mutants of Bacillus subtilis and show that it could easily and automatically reproduce the statistical analysis of the cognate publication. Furthermore, by mining the correlation matrices, k-means clusters and heatmaps generated by T-REx we observed interesting gene-behavior and identified sub-groups in the CodY regulon.ConclusionT-REx is a parameter-free statistical analysis pipeline for RNA-seq gene expression data that is dedicated for use by biologists and bioinformaticians alike. The tables and figures produced by T-REx are in most cases sufficient to accurately mine the statistical results. In addition to the stand-alone version, we offer a user-friendly webserver that only needs basic input (http://genome2d.molgenrug.nl).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1834-4) contains supplementary material, which is available to authorized users.

High‐throughput CRISPRi phenotyping identifies new essential genes inStreptococcus pneumoniae

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High-throughput CRISPRi phenotyping inStreptococcus pneumoniaeidentifies new essential genes involved in cell wall synthesis and competence development

“…To test the precision of CRISPRi in S. pneumoniae , we determined the transcriptome of the sgRNA luc strain (Strain XL28) by RNA-Seq in the presence or absence of IPTG. The data was analyzed using Rockhopper (McClure et al, 2013) and T-REx (de Jong et al, 2015). The RNA-Seq data showed that expression of dCas9 was stringently repressed by LacI without IPTG, and was upregulated ~600 fold upon addition of 1 mM IPTG after 2.5 hr.…”

Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus

“…After trimming the raw RNA-seq reads (PE150 (paired-end 150 bp)) from the adapter sequences, reads were mapped against the B. cereus ATCC 14579 genome sequence. The RPKM (reads per kilo base per million mapped reads) table was generated, and differential gene expression analyses were carried out with the webserver pipeline T-Rex [60] on the Genome2D webserver (http://genome2d.molgenrug.nl/). The significance threshold was defined by a p-value□of <□0.05 and a fold-change of >2 (“TopHits” in T-REx).…”