%\VignetteIndexEntry{TBX20 RNA-Seq data subset}
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%\VignettePackage{RNASeqDataSubset}
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\title{TBX20 RNA-Seq data subset}
\author{Daniel Bindreither}

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\begin{document}

\maketitle

\section{Introduction}

The TBX20 data set \cite{Sakabe10022012} provides ChIP-Seq and RNA-Seq
data. In here only the RNA-Seq part of the data is utilized. The raw
data where downloaded from Gene Expression Omnibus (GEO)
\cite{Barrett01012011}, accession number GSM767225-GSM767230.
TBX20 (T-box 20) in general is a transcriptional regulator essential for cardiac
development and maintenance of mouse heart tissue. In this study TXB20
was knocked-out by using a Tamoxifen mediated conditional knock-out
system. Transcriptional changes caused by the ablation of the second
exon of TBX20 result in rapid onset of heart failures and the
subsequent death of the mice. TBX20 knock-out adult heart tissue was
compared to wild type adult heart tissue. This package provides a
subset of the RNA-Seq data (chromosome 19) for demonstrating the capabilities 
of the \Rpackage{SpliceGraph} package. The vignette describes how to 
access the phenotypic data and the raw reads aligned with Bowtie \cite{Bowtie19261174}
to the mm9 assembly of \textit{Mus musculus} from UCSC Genome 
Browser \cite{Fujita18102010}.

Accessing the experimental design ...

<<>>=
library("RNASeqDataSubset")
fn <- system.file("extdata", "phenoData.txt", 
                  package="RNASeqDataSubset")
pd <- read.table(fn, header=TRUE,
                 stringsAsFactors=FALSE)
@ 


<<results=tex, echo=FALSE>>=
library(xtable)
pd <- xtable(pd, caption="Design of the TBX20 experiment")
print(pd)
@ 

Accessing the raw reads ...

<<>>=
library("Rsamtools")
fls <- getBamFileList()
bfs <- BamFileList(fls)
@ 


\bibliography{RNASeqDataSubset}
\bibliographystyle{plain}


\section{Session Information}

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sessionInfo()
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\end{document}
