arab: Arabidopsis RNA-Seq Data Set

arabR Documentation

Arabidopsis RNA-Seq Data Set


An RNA-Seq dataset from a pilot study of the defense response of Arabidopsis to infection by bacteria. We performed RNA-Seq experiments on three independent biological samples from each of the two treatment groups. The matrix contains the frequencies of RNA-Seq reads mapped to genes in a reference database. Rows correspond to genes and columns correspond to independent biological samples.




A 26222 by 6 matrix of RNA-Seq read frequencies.


We challenged leaves of Arabidopsis with the defense-eliciting ΔhrcC mutant of Pseudomonas syringae pathovar tomato DC3000. We also infiltrated leaves of Arabidopsis with 10mM MgCl2 as a mock inoculation. RNA was isolated 7 hours after inoculation, enriched for mRNA and prepared for RNA-Seq. We sequenced one replicate per channel on the Illumina Genome Analyzer ( The length of the RNA-Seq reads can vary in length depending on user preference and the sequencing instrument. The dataset used here are derived from a 36-cycle sequencing reaction, that we trimmed to 25mers. We used an in-house computational pipeline to process, align, and assign RNA-Seq reads to genes according to a reference database we developed for Arabidopsis.


Jason S Cumbie and Jeff H Chang


Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq", Statistical Applications in Genetics and Molecular Biology, 10 (1).

NBPSeq documentation built on June 9, 2022, 5:06 p.m.