arab {NBPSeq} | R Documentation |
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.
Usage
data(arab)
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.
Author(s)
Jason S Cumbie cumbiej@onid.orst.edu and Jeff H Chang changj@cgrb.oregonstate.edu.
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).