Transcriptomics

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Transcription profiling by array of Arabidopsis after inoculation with Pseudomonas syringae DC3000 hrcC mutant


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 derived from Arabidopsis thaliana infected with a strain of defense-eliciting bacteria. We identified 308 genes that were differentially induced. Using alternative methods, we provided support for the induced expression and biological relevance of a substantial proportion of the genes. These results suggest the NBP parameterization of the negative binomial distribution is well suited for explaining RNA-Seq data and the statistical test makes GENE-counter a powerful pipeline for studying genome-wide expression changes. GENE-counter is freely available at http://changlab.cgrb.oregonstate.edu/. Our RNA-seq data is uploaded on the NCBI short read archive (SRA) under the SRA025952. 6 samples total. Two treatments with three biological replicates each. MgCl2 is the mock treatment, and hrcC is the experimental treatment.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Todd C Mockler  James C Carrington   Yanming Di   Jason S Cumbie   Larry J Wilhelm   Jeffrey A Kimbrel   Christopher M Sullivan   Jeff Chang   Samuel E Fox   Aron D Curzon   Daniel W Schafer    

PROVIDER: E-GEOD-25818 | ArrayExpress | 2010-12-03

SECONDARY ACCESSION(S): GSE25818PRJNA135627

REPOSITORIES: GEO, ArrayExpress

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Publications

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Cumbie Jason S JS   Kimbrel Jeffrey A JA   Di Yanming Y   Schafer Daniel W DW   Wilhelm Larry J LJ   Fox Samuel E SE   Sullivan Christopher M CM   Curzon Aron D AD   Carrington James C JC   Mockler Todd C TC   Chang Jeff H JH  

PloS one 20111006 10


GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference. To a  ...[more]

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