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<h2>RNA-Seq anaysis of cytokinin-treated rice seedling roots and shoots</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>.</p>
<p>Analysis of alternative splicing revealed by this data set is described in <a href="https://www.ncbi.nlm.nih.gov/pubmed/31245776">Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing</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>
<h3>Visualization</h3>
<p>
To visualize these data in <a href="https://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>.
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[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[ ]BA2h-R3.bam.bai2017-07-25 15:04 570KIndex for binary alignments (bam) file
[ ]Control2h-R1.bedgraph.gz.tbi2017-07-25 15:04 259KBedGraph (wiggle) format file
[ ]Control2h-S1.bed.gz2017-07-25 15:04 2.8MAnnotation or junction file
[ ]Control2h-S3.FJ.bed.gz2017-07-25 15:04 2.5MLoraine Lab FindJunctions file
[ ]Control2h-S3.bam.bai2017-07-25 15:04 567KIndex for binary alignments (bam) file
[ ]Control2h-S3.bed.gz.tbi2017-07-25 15:04 149KTabix index file
[ ]Control2h-R1.bedgraph.gz2017-07-25 15:04 134MBedGraph (wiggle) format file
[ ]Control2h-S3.FJ.bed.gz.tbi2017-07-25 15:04 144KTabix index file
[ ]Control2h-S3.bedgraph.gz.tbi2017-07-25 15:04 242KBedGraph (wiggle) format file
[ ]BA2h-R2.bedgraph.gz.tbi2017-07-25 15:05 253KBedGraph (wiggle) format file
[ ]BA2h-R3.bedgraph.gz.tbi2017-07-25 15:05 243KBedGraph (wiggle) format file
[ ]BA2h-S1.bed.gz2017-07-25 15:05 2.9MAnnotation or junction file
[ ]BA2h-S2.FJ.bed.gz.tbi2017-07-25 15:05 144KTabix index file
[ ]BA2h-S2.bedgraph.gz.tbi2017-07-25 15:05 245KBedGraph (wiggle) format file
[ ]BA2h-S3.bam.bai2017-07-25 15:05 554KIndex for binary alignments (bam) file
[ ]Control2h-R1.FJ.bed.gz2017-07-25 15:05 2.6MLoraine Lab FindJunctions file
[ ]Control2h-R1.FJ.bed.gz.tbi2017-07-25 15:05 148KTabix index file
[ ]Control2h-R1.bam2017-07-25 15:05 3.2GBinary alignments file
[ ]Control2h-R1.bed.gz2017-07-25 15:05 3.0MAnnotation or junction file
[ ]Control2h-R3.bed.gz.tbi2017-07-25 15:05 150KTabix index file
[ ]Control2h-S1.bed.gz.tbi2017-07-25 15:05 150KTabix index file
[ ]Control2h-S3.bed.gz2017-07-25 15:05 2.8MAnnotation or junction file
[ ]BA2h-R1.bedgraph.gz2017-07-25 15:05 123MBedGraph (wiggle) format file
[ ]BA2h-S1.FJ.bed.gz.tbi2017-07-25 15:05 145KTabix index file
[ ]BA2h-S2.bed.gz.tbi2017-07-25 15:05 149KTabix index file
[ ]BA2h-S3.bed.gz.tbi2017-07-25 15:05 148KTabix index file
[ ]Control2h-R1.bed.gz.tbi2017-07-25 15:05 153KTabix index file
[ ]Control2h-S2.bam2017-07-25 15:05 2.4GBinary alignments file
[ ]Control2h-S2.bedgraph.gz.tbi2017-07-25 15:05 244KBedGraph (wiggle) format file
[ ]Control2h-R3.bam2017-07-25 15:06 2.0GBinary alignments file
[ ]BA2h-R3.FJ.bed.gz.tbi2017-07-25 15:06 144KTabix index file
[ ]BA2h-R3.bedgraph.gz2017-07-25 15:06 106MBedGraph (wiggle) format file
[ ]Control2h-R2.bam.bai2017-07-25 15:06 625KIndex for binary alignments (bam) file
[ ]Control2h-S1.bam.bai2017-07-25 15:06 582KIndex for binary alignments (bam) file
[ ]Control2h-S2.FJ.bed.gz2017-07-25 15:06 2.5MLoraine Lab FindJunctions file
[ ]BA2h-R2.bedgraph.gz2017-07-25 15:06 119MBedGraph (wiggle) format file
[ ]Control2h-R3.FJ.bed.gz2017-07-25 15:06 2.4MLoraine Lab FindJunctions file
[ ]Control2h-S1.bam2017-07-25 15:06 2.4GBinary alignments file
[ ]BA2h-R1.bam2017-07-25 15:07 2.9GBinary alignments file
[ ]BA2h-R3.FJ.bed.gz2017-07-25 15:07 2.4MLoraine Lab FindJunctions file
[ ]Control2h-R2.bedgraph.gz2017-07-25 15:07 127MBedGraph (wiggle) format file
[ ]BA2h-S1.bedgraph.gz2017-07-25 15:07 114MBedGraph (wiggle) format file
[ ]BA2h-S3.bedgraph.gz.tbi2017-07-25 15:07 238KBedGraph (wiggle) format file
[ ]Control2h-S1.FJ.bed.gz.tbi2017-07-25 15:07 144KTabix index file
[ ]Control2h-S1.bedgraph.gz2017-07-25 15:07 108MBedGraph (wiggle) format file
[ ]BA2h-R2.bed.gz.tbi2017-07-25 15:08 153KTabix index file
[ ]BA2h-R3.bam2017-07-25 15:08 2.1GBinary alignments file
[ ]BA2h-S1.bed.gz.tbi2017-07-25 15:08 151KTabix index file
[ ]BA2h-R1.FJ.bed.gz.tbi2017-07-25 15:08 146KTabix index file
[ ]BA2h-S2.bam2017-07-25 15:08 2.5GBinary alignments file
[ ]Control2h-S2.bam.bai2017-07-25 15:08 585KIndex for binary alignments (bam) file
[ ]BA2h-R1.FJ.bed.gz2017-07-25 15:08 2.5MLoraine Lab FindJunctions file
[ ]BA2h-R2.bam.bai2017-07-25 15:08 612KIndex for binary alignments (bam) file
[ ]BA2h-R3.bed.gz.tbi2017-07-25 15:08 150KTabix index file
[ ]BA2h-S1.FJ.bed.gz2017-07-25 15:08 2.5MLoraine Lab FindJunctions file
[ ]BA2h-S3.FJ.bed.gz2017-07-25 15:08 2.4MLoraine Lab FindJunctions file
[ ]BA2h-S3.bed.gz2017-07-25 15:08 2.7MAnnotation or junction file
[ ]Control2h-R1.bam.bai2017-07-25 15:08 633KIndex for binary alignments (bam) file
[ ]Control2h-R2.bed.gz2017-07-25 15:08 3.0MAnnotation or junction file
[ ]Control2h-R3.bed.gz2017-07-25 15:08 2.8MAnnotation or junction file
[ ]BA2h-R2.bed.gz2017-07-25 15:08 2.9MAnnotation or junction file
[ ]BA2h-S3.FJ.bed.gz.tbi2017-07-25 15:08 142KTabix index file
[ ]BA2h-S2.FJ.bed.gz2017-07-25 15:08 2.5MLoraine Lab FindJunctions file
[ ]BA2h-S2.bam.bai2017-07-25 15:08 586KIndex for binary alignments (bam) file
[ ]BA2h-S2.bed.gz2017-07-25 15:08 2.8MAnnotation or junction file
[ ]Control2h-R3.bam.bai2017-07-25 15:08 571KIndex for binary alignments (bam) file
[ ]Control2h-S2.bed.gz.tbi2017-07-25 15:08 150KTabix index file
[ ]Control2h-S2.bedgraph.gz2017-07-25 15:08 108MBedGraph (wiggle) format file
[ ]BA2h-R2.bam2017-07-25 15:09 2.7GBinary alignments file
[ ]BA2h-R3.bed.gz2017-07-25 15:09 2.8MAnnotation or junction file
[ ]BA2h-S3.bam2017-07-25 15:09 1.9GBinary alignments file
[ ]Control2h-S3.bam2017-07-25 15:10 2.2GBinary alignments file
[ ]BA2h-R2.FJ.bed.gz.tbi2017-07-25 15:10 147KTabix index file
[ ]BA2h-S2.bedgraph.gz2017-07-25 15:10 108MBedGraph (wiggle) format file
[ ]Control2h-R2.bed.gz.tbi2017-07-25 15:10 153KTabix index file
[ ]Control2h-S1.FJ.bed.gz2017-07-25 15:10 2.5MLoraine Lab FindJunctions file
[ ]Control2h-S2.bed.gz2017-07-25 15:10 2.8MAnnotation or junction file
[ ]BA2h-S3.bedgraph.gz2017-07-25 15:10 99MBedGraph (wiggle) format file
[ ]Control2h-R3.bedgraph.gz2017-07-25 15:10 106MBedGraph (wiggle) format file
[ ]BA2h-R1.bam.bai2017-07-25 15:10 618KIndex for binary alignments (bam) file
[ ]BA2h-R1.bed.gz2017-07-25 15:10 2.9MAnnotation or junction file
[ ]BA2h-S1.bam2017-07-25 15:10 2.7GBinary alignments file
[ ]Control2h-R2.FJ.bed.gz.tbi2017-07-25 15:10 147KTabix index file
[ ]BA2h-R1.bed.gz.tbi2017-07-25 15:10 152KTabix index file
[ ]BA2h-R1.bedgraph.gz.tbi2017-07-25 15:10 250KBedGraph (wiggle) format file
[ ]BA2h-S1.bam.bai2017-07-25 15:10 597KIndex for binary alignments (bam) file
[ ]Control2h-R2.FJ.bed.gz2017-07-25 15:10 2.6MLoraine Lab FindJunctions file
[ ]Control2h-S3.bedgraph.gz2017-07-25 15:10 108MBedGraph (wiggle) format file
[ ]BA2h-R2.FJ.bed.gz2017-07-25 15:11 2.5MLoraine Lab FindJunctions file
[ ]BA2h-S1.bedgraph.gz.tbi2017-07-25 15:11 248KBedGraph (wiggle) format file
[ ]Control2h-R2.bam2017-07-25 15:11 3.0GBinary alignments file
[ ]Control2h-R2.bedgraph.gz.tbi2017-07-25 15:11 255KBedGraph (wiggle) format file
[ ]Control2h-R3.FJ.bed.gz.tbi2017-07-25 15:11 144KTabix index file
[ ]Control2h-R3.bedgraph.gz.tbi2017-07-25 15:11 238KBedGraph (wiggle) format file
[ ]Control2h-S1.bedgraph.gz.tbi2017-07-25 15:11 246KBedGraph (wiggle) format file
[ ]Control2h-S2.FJ.bed.gz.tbi2017-07-25 15:11 144KTabix index file