Gene expression analysis of Arabidopsis thaliana infected with Pseudomonas syringae, a strain of defense-eliciting bacteria

ABSTRACT: RNA-Sequencing is a transformative method that captures the quantitative dynamics of a transcriptome with exquisite sensitivity and single-base resolution. There are, however, few computational pipelines for RNA-Seq with statistical tests that evince sufficient robustness and power as demanded by the difficult combination of small sample sizes and high variability in sequence read counts. To this end, we developed GENE-counter, a complete software pipeline for analyzing RNA-Seq data for genome-wide expression differences between replicated treatment groups. One important component of GENE-counter is a statistical test based on the NBP parameterization of the negative binomial distribution for identifying differentially expressed genome features. We used GENE-counter to analyze RNA-Seq data

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jeff Chang 

PROVIDER: E-GEOD-25818 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress