arab: Arabidopsis RNA-Seq Data Set
Description
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.format
A 26222 by 6 matrix of RNA-Seq read frequencies.Details
We challenged leaves of Arabidopsis with the defense-eliciting
$\Delta$hrcC 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 (http://www.illumina.com). 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.References
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).