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<h2>Identification of cytokinin-reponsive genes using RNA-Seq</h2>
<p>
This directory contains processed data from an RNA-Seq experiment
investigating the effects of exogenous cytokinin (BA) treatment on
gene expression in 10-day old rice seedlings.
</p>
<p>
Differential expression analysis of these data are described in <a href="https://www.ncbi.nlm.nih.gov/pubmed/27931185">Characterization of the cytokinin-responsive transcriptome in rice</a>. Analysis of alternative splicing revealed by this data set is not yet published and is underway.
</p>
<p>
Students in the Loraine Lab (which generated these data) are preparing a manuscript analyzing alternative splicing in this data set. <b>For this reason, we request that you not use these data to investigate alternative splicing in rice -- please give our students a chance to finish and get credit for their hard work.</b> For more details or to explore a possible collaboration, please contact <a href="mailto:aloraine@uncc.edu">Ann Loraine</a>. 
</p>
<p>
<h3>Samples:</h3>
<ul>
<li>BA2h-R1 - BA-treated roots, replicate 1
<li>BA2h-R2 - BA-treated roots, replicate 2
<li>BA2h-R3 - BA-treated roots, replicate 3
<li>BA2h-S1 - BA-treated shoots, replicate 1
<li>BA2h-S2 - BA-treated shoots, replicate 2
<li>BA2h-S3 - BA-treated shoots, replicate 3
<li>Control2h-R1 - mock-treated roots, replicate 1
<li>Control2h-R2 - mock-treated roots, replicate 2
<li>Control2h-R3 - mock-treated roots, replicate 3
<li>Control2h-S1 - mock-treated shoots, replicate 1
<li>Control2h-S2 - mock-treated shoots, replicate 2
<li>Control2h-S3 - mock-treated shoots, replicate 3
</ul>
</p>
<p>
Reads were aligned on the genome TopHat. Reads mapping once or multiple times were
segregated into BAM (binary alignment files) with extensions .sm.bam
and .mm.bam respectively. The single-mapping reads whose alignments
contained gaps indicating alignment to an exon-exon junction were
further processed using FindJunctions, developed in
the Loraine lab and available from a repository hosted on BitBucket. FindJunctions was run with options -n 5 (flanking 5)
and -u (unique) ensuring that junctions were supported by
uniquely-mapping reads only with at least five bases aligned to the
flanking exons.
</p>
<h3>File types and their extensions include:</h3>
</p>
<ul>
<li>.bam file - binary alignments file from tophat
<li>.bedgraph.gz file - read coverage graph
<li>.FJ.bed.gz - FindJunctions junctions file; score indicates the number of spliced reads supporting a junction
<li>.bed.gz - Tophat junction file; score indicates the number of spliced reads supporting a junction
<li>.alignments.txt.gz - tabulates reads and alignments
</ul>
<h3>Visualization</h3>
<p>
To visualize these data in <a href="http://www.bioviz.org">Integrated
Genome Browser</a>, launch the program and choose the
O_sativa_japonica_Oct_2011 genome. After the gene models load, open
data files in the folder named <b>RNA-Seq</b>.
</p>

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[ICO]NameLast modifiedSizeDescription
[DIR]Parent Directory  -  
[   ]BA2h-R1.FJ.bed.gz25-Jul-2017 15:08 2.5MLoraine Lab FindJunctions file
[   ]BA2h-R1.FJ.bed.gz.tbi25-Jul-2017 15:08 146KTabix index file
[   ]BA2h-R1.bam25-Jul-2017 15:07 2.9GBinary alignments file
[   ]BA2h-R1.bam.bai25-Jul-2017 15:10 618KIndex for binary alignments (bam) file
[   ]BA2h-R1.bed.gz25-Jul-2017 15:10 2.9MAnnotation or junction file
[   ]BA2h-R1.bed.gz.tbi25-Jul-2017 15:10 152KTabix index file
[   ]BA2h-R1.bedgraph.gz25-Jul-2017 15:05 123MBedGraph (wiggle) format file
[   ]BA2h-R1.bedgraph.gz.tbi25-Jul-2017 15:10 250KBedGraph (wiggle) format file
[   ]BA2h-R2.FJ.bed.gz25-Jul-2017 15:11 2.5MLoraine Lab FindJunctions file
[   ]BA2h-R2.FJ.bed.gz.tbi25-Jul-2017 15:10 147KTabix index file
[   ]BA2h-R2.bam25-Jul-2017 15:09 2.7GBinary alignments file
[   ]BA2h-R2.bam.bai25-Jul-2017 15:08 612KIndex for binary alignments (bam) file
[   ]BA2h-R2.bed.gz25-Jul-2017 15:08 2.9MAnnotation or junction file
[   ]BA2h-R2.bed.gz.tbi25-Jul-2017 15:08 153KTabix index file
[   ]BA2h-R2.bedgraph.gz25-Jul-2017 15:06 119MBedGraph (wiggle) format file
[   ]BA2h-R2.bedgraph.gz.tbi25-Jul-2017 15:05 253KBedGraph (wiggle) format file
[   ]BA2h-R3.FJ.bed.gz25-Jul-2017 15:07 2.4MLoraine Lab FindJunctions file
[   ]BA2h-R3.FJ.bed.gz.tbi25-Jul-2017 15:06 144KTabix index file
[   ]BA2h-R3.bam25-Jul-2017 15:08 2.1GBinary alignments file
[   ]BA2h-R3.bam.bai25-Jul-2017 15:04 570KIndex for binary alignments (bam) file
[   ]BA2h-R3.bed.gz25-Jul-2017 15:09 2.8MAnnotation or junction file
[   ]BA2h-R3.bed.gz.tbi25-Jul-2017 15:08 150KTabix index file
[   ]BA2h-R3.bedgraph.gz25-Jul-2017 15:06 106MBedGraph (wiggle) format file
[   ]BA2h-R3.bedgraph.gz.tbi25-Jul-2017 15:05 243KBedGraph (wiggle) format file
[   ]BA2h-S1.FJ.bed.gz25-Jul-2017 15:08 2.5MLoraine Lab FindJunctions file
[   ]BA2h-S1.FJ.bed.gz.tbi25-Jul-2017 15:05 145KTabix index file
[   ]BA2h-S1.bam25-Jul-2017 15:10 2.7GBinary alignments file
[   ]BA2h-S1.bam.bai25-Jul-2017 15:10 597KIndex for binary alignments (bam) file
[   ]BA2h-S1.bed.gz25-Jul-2017 15:05 2.9MAnnotation or junction file
[   ]BA2h-S1.bed.gz.tbi25-Jul-2017 15:08 151KTabix index file
[   ]BA2h-S1.bedgraph.gz25-Jul-2017 15:07 114MBedGraph (wiggle) format file
[   ]BA2h-S1.bedgraph.gz.tbi25-Jul-2017 15:11 248KBedGraph (wiggle) format file
[   ]BA2h-S2.FJ.bed.gz25-Jul-2017 15:08 2.5MLoraine Lab FindJunctions file
[   ]BA2h-S2.FJ.bed.gz.tbi25-Jul-2017 15:05 144KTabix index file
[   ]BA2h-S2.bam25-Jul-2017 15:08 2.5GBinary alignments file
[   ]BA2h-S2.bam.bai25-Jul-2017 15:08 586KIndex for binary alignments (bam) file
[   ]BA2h-S2.bed.gz25-Jul-2017 15:08 2.8MAnnotation or junction file
[   ]BA2h-S2.bed.gz.tbi25-Jul-2017 15:05 149KTabix index file
[   ]BA2h-S2.bedgraph.gz25-Jul-2017 15:10 108MBedGraph (wiggle) format file
[   ]BA2h-S2.bedgraph.gz.tbi25-Jul-2017 15:05 245KBedGraph (wiggle) format file
[   ]BA2h-S3.FJ.bed.gz25-Jul-2017 15:08 2.4MLoraine Lab FindJunctions file
[   ]BA2h-S3.FJ.bed.gz.tbi25-Jul-2017 15:08 142KTabix index file
[   ]BA2h-S3.bam25-Jul-2017 15:09 1.9GBinary alignments file
[   ]BA2h-S3.bam.bai25-Jul-2017 15:05 554KIndex for binary alignments (bam) file
[   ]BA2h-S3.bed.gz25-Jul-2017 15:08 2.7MAnnotation or junction file
[   ]BA2h-S3.bed.gz.tbi25-Jul-2017 15:05 148KTabix index file
[   ]BA2h-S3.bedgraph.gz25-Jul-2017 15:10 99MBedGraph (wiggle) format file
[   ]BA2h-S3.bedgraph.gz.tbi25-Jul-2017 15:07 238KBedGraph (wiggle) format file
[   ]Control2h-R1.FJ.bed.gz25-Jul-2017 15:05 2.6MLoraine Lab FindJunctions file
[   ]Control2h-R1.FJ.bed.gz.tbi25-Jul-2017 15:05 148KTabix index file
[   ]Control2h-R1.bam25-Jul-2017 15:05 3.2GBinary alignments file
[   ]Control2h-R1.bam.bai25-Jul-2017 15:08 633KIndex for binary alignments (bam) file
[   ]Control2h-R1.bed.gz25-Jul-2017 15:05 3.0MAnnotation or junction file
[   ]Control2h-R1.bed.gz.tbi25-Jul-2017 15:05 153KTabix index file
[   ]Control2h-R1.bedgraph.gz25-Jul-2017 15:04 134MBedGraph (wiggle) format file
[   ]Control2h-R1.bedgraph.gz.tbi25-Jul-2017 15:04 259KBedGraph (wiggle) format file
[   ]Control2h-R2.FJ.bed.gz25-Jul-2017 15:10 2.6MLoraine Lab FindJunctions file
[   ]Control2h-R2.FJ.bed.gz.tbi25-Jul-2017 15:10 147KTabix index file
[   ]Control2h-R2.bam25-Jul-2017 15:11 3.0GBinary alignments file
[   ]Control2h-R2.bam.bai25-Jul-2017 15:06 625KIndex for binary alignments (bam) file
[   ]Control2h-R2.bed.gz25-Jul-2017 15:08 3.0MAnnotation or junction file
[   ]Control2h-R2.bed.gz.tbi25-Jul-2017 15:10 153KTabix index file
[   ]Control2h-R2.bedgraph.gz25-Jul-2017 15:07 127MBedGraph (wiggle) format file
[   ]Control2h-R2.bedgraph.gz.tbi25-Jul-2017 15:11 255KBedGraph (wiggle) format file
[   ]Control2h-R3.FJ.bed.gz25-Jul-2017 15:06 2.4MLoraine Lab FindJunctions file
[   ]Control2h-R3.FJ.bed.gz.tbi25-Jul-2017 15:11 144KTabix index file
[   ]Control2h-R3.bam25-Jul-2017 15:06 2.0GBinary alignments file
[   ]Control2h-R3.bam.bai25-Jul-2017 15:08 571KIndex for binary alignments (bam) file
[   ]Control2h-R3.bed.gz25-Jul-2017 15:08 2.8MAnnotation or junction file
[   ]Control2h-R3.bed.gz.tbi25-Jul-2017 15:05 150KTabix index file
[   ]Control2h-R3.bedgraph.gz25-Jul-2017 15:10 106MBedGraph (wiggle) format file
[   ]Control2h-R3.bedgraph.gz.tbi25-Jul-2017 15:11 238KBedGraph (wiggle) format file
[   ]Control2h-S1.FJ.bed.gz25-Jul-2017 15:10 2.5MLoraine Lab FindJunctions file
[   ]Control2h-S1.FJ.bed.gz.tbi25-Jul-2017 15:07 144KTabix index file
[   ]Control2h-S1.bam25-Jul-2017 15:06 2.4GBinary alignments file
[   ]Control2h-S1.bam.bai25-Jul-2017 15:06 582KIndex for binary alignments (bam) file
[   ]Control2h-S1.bed.gz25-Jul-2017 15:04 2.8MAnnotation or junction file
[   ]Control2h-S1.bed.gz.tbi25-Jul-2017 15:05 150KTabix index file
[   ]Control2h-S1.bedgraph.gz25-Jul-2017 15:07 108MBedGraph (wiggle) format file
[   ]Control2h-S1.bedgraph.gz.tbi25-Jul-2017 15:11 246KBedGraph (wiggle) format file
[   ]Control2h-S2.FJ.bed.gz25-Jul-2017 15:06 2.5MLoraine Lab FindJunctions file
[   ]Control2h-S2.FJ.bed.gz.tbi25-Jul-2017 15:11 144KTabix index file
[   ]Control2h-S2.bam25-Jul-2017 15:05 2.4GBinary alignments file
[   ]Control2h-S2.bam.bai25-Jul-2017 15:08 585KIndex for binary alignments (bam) file
[   ]Control2h-S2.bed.gz25-Jul-2017 15:10 2.8MAnnotation or junction file
[   ]Control2h-S2.bed.gz.tbi25-Jul-2017 15:08 150KTabix index file
[   ]Control2h-S2.bedgraph.gz25-Jul-2017 15:08 108MBedGraph (wiggle) format file
[   ]Control2h-S2.bedgraph.gz.tbi25-Jul-2017 15:05 244KBedGraph (wiggle) format file
[   ]Control2h-S3.FJ.bed.gz25-Jul-2017 15:04 2.5MLoraine Lab FindJunctions file
[   ]Control2h-S3.FJ.bed.gz.tbi25-Jul-2017 15:04 144KTabix index file
[   ]Control2h-S3.bam25-Jul-2017 15:10 2.2GBinary alignments file
[   ]Control2h-S3.bam.bai25-Jul-2017 15:04 567KIndex for binary alignments (bam) file
[   ]Control2h-S3.bed.gz25-Jul-2017 15:05 2.8MAnnotation or junction file
[   ]Control2h-S3.bed.gz.tbi25-Jul-2017 15:04 149KTabix index file
[   ]Control2h-S3.bedgraph.gz25-Jul-2017 15:10 108MBedGraph (wiggle) format file
[   ]Control2h-S3.bedgraph.gz.tbi25-Jul-2017 15:04 242KBedGraph (wiggle) format file
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