RNA-Seq anaysis of cytokinin-treated rice seedling roots and shoots

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.

Differential expression analysis of these data are described in Characterization of the cytokinin-responsive transcriptome in rice.

Analysis of alternative splicing revealed by this data set is described in Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing.

Samples:

Visualization

To visualize these data in Integrated Genome Browser, launch the program and choose the O_sativa_japonica_Oct_2011 genome. After the gene models load, open data files in the folder named RNA-Seq.

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[   ]Control2h-R1.bam2017-07-25 15:05 3.2GBinary alignments file
[   ]Control2h-R2.bam2017-07-25 15:11 3.0GBinary alignments file
[   ]BA2h-R1.bam2017-07-25 15:07 2.9GBinary alignments file
[   ]BA2h-S1.bam2017-07-25 15:10 2.7GBinary alignments file
[   ]BA2h-R2.bam2017-07-25 15:09 2.7GBinary alignments file
[   ]BA2h-S2.bam2017-07-25 15:08 2.5GBinary alignments file
[   ]Control2h-S2.bam2017-07-25 15:05 2.4GBinary alignments file
[   ]Control2h-S1.bam2017-07-25 15:06 2.4GBinary alignments file
[   ]Control2h-S3.bam2017-07-25 15:10 2.2GBinary alignments file
[   ]BA2h-R3.bam2017-07-25 15:08 2.1GBinary alignments file
[   ]Control2h-R3.bam2017-07-25 15:06 2.0GBinary alignments file
[   ]BA2h-S3.bam2017-07-25 15:09 1.9GBinary alignments file
[   ]Control2h-R1.bedgraph.gz2017-07-25 15:04 134MBedGraph (wiggle) format file
[   ]Control2h-R2.bedgraph.gz2017-07-25 15:07 127MBedGraph (wiggle) format file
[   ]BA2h-R1.bedgraph.gz2017-07-25 15:05 123MBedGraph (wiggle) format file
[   ]BA2h-R2.bedgraph.gz2017-07-25 15:06 119MBedGraph (wiggle) format file
[   ]BA2h-S1.bedgraph.gz2017-07-25 15:07 114MBedGraph (wiggle) format file
[   ]Control2h-S2.bedgraph.gz2017-07-25 15:08 108MBedGraph (wiggle) format file
[   ]BA2h-S2.bedgraph.gz2017-07-25 15:10 108MBedGraph (wiggle) format file
[   ]Control2h-S1.bedgraph.gz2017-07-25 15:07 108MBedGraph (wiggle) format file
[   ]Control2h-S3.bedgraph.gz2017-07-25 15:10 108MBedGraph (wiggle) format file
[   ]BA2h-R3.bedgraph.gz2017-07-25 15:06 106MBedGraph (wiggle) format file
[   ]Control2h-R3.bedgraph.gz2017-07-25 15:10 106MBedGraph (wiggle) format file
[   ]BA2h-S3.bedgraph.gz2017-07-25 15:10 99MBedGraph (wiggle) format file
[   ]Control2h-R1.bed.gz2017-07-25 15:05 3.0MAnnotation or junction file
[   ]Control2h-R2.bed.gz2017-07-25 15:08 3.0MAnnotation or junction file
[   ]BA2h-R2.bed.gz2017-07-25 15:08 2.9MAnnotation or junction file
[   ]BA2h-R1.bed.gz2017-07-25 15:10 2.9MAnnotation or junction file
[   ]BA2h-S1.bed.gz2017-07-25 15:05 2.9MAnnotation or junction file
[   ]BA2h-S2.bed.gz2017-07-25 15:08 2.8MAnnotation or junction file
[   ]Control2h-S1.bed.gz2017-07-25 15:04 2.8MAnnotation or junction file
[   ]Control2h-S2.bed.gz2017-07-25 15:10 2.8MAnnotation or junction file
[   ]Control2h-S3.bed.gz2017-07-25 15:05 2.8MAnnotation or junction file
[   ]Control2h-R3.bed.gz2017-07-25 15:08 2.8MAnnotation or junction file
[   ]BA2h-R3.bed.gz2017-07-25 15:09 2.8MAnnotation or junction file
[   ]BA2h-S3.bed.gz2017-07-25 15:08 2.7MAnnotation or junction file
[   ]Control2h-R1.FJ.bed.gz2017-07-25 15:05 2.6MLoraine Lab FindJunctions file
[   ]Control2h-R2.FJ.bed.gz2017-07-25 15:10 2.6MLoraine Lab FindJunctions file
[   ]BA2h-R2.FJ.bed.gz2017-07-25 15:11 2.5MLoraine Lab FindJunctions file
[   ]BA2h-R1.FJ.bed.gz2017-07-25 15:08 2.5MLoraine Lab FindJunctions file
[   ]BA2h-S1.FJ.bed.gz2017-07-25 15:08 2.5MLoraine Lab FindJunctions file
[   ]Control2h-S1.FJ.bed.gz2017-07-25 15:10 2.5MLoraine Lab FindJunctions file
[   ]BA2h-S2.FJ.bed.gz2017-07-25 15:08 2.5MLoraine Lab FindJunctions file
[   ]Control2h-S2.FJ.bed.gz2017-07-25 15:06 2.5MLoraine Lab FindJunctions file
[   ]Control2h-S3.FJ.bed.gz2017-07-25 15:04 2.5MLoraine Lab FindJunctions file
[   ]Control2h-R3.FJ.bed.gz2017-07-25 15:06 2.4MLoraine Lab FindJunctions file
[   ]BA2h-R3.FJ.bed.gz2017-07-25 15:07 2.4MLoraine Lab FindJunctions file
[   ]BA2h-S3.FJ.bed.gz2017-07-25 15:08 2.4MLoraine Lab FindJunctions file
[   ]Control2h-R1.bam.bai2017-07-25 15:08 633KIndex for binary alignments (bam) file
[   ]Control2h-R2.bam.bai2017-07-25 15:06 625KIndex for binary alignments (bam) file
[   ]BA2h-R1.bam.bai2017-07-25 15:10 618KIndex for binary alignments (bam) file
[   ]BA2h-R2.bam.bai2017-07-25 15:08 612KIndex for binary alignments (bam) file
[   ]BA2h-S1.bam.bai2017-07-25 15:10 597KIndex for binary alignments (bam) file
[   ]BA2h-S2.bam.bai2017-07-25 15:08 586KIndex for binary alignments (bam) file
[   ]Control2h-S2.bam.bai2017-07-25 15:08 585KIndex for binary alignments (bam) file
[   ]Control2h-S1.bam.bai2017-07-25 15:06 582KIndex for binary alignments (bam) file
[   ]Control2h-R3.bam.bai2017-07-25 15:08 571KIndex for binary alignments (bam) file
[   ]BA2h-R3.bam.bai2017-07-25 15:04 570KIndex for binary alignments (bam) file
[   ]Control2h-S3.bam.bai2017-07-25 15:04 567KIndex for binary alignments (bam) file
[   ]BA2h-S3.bam.bai2017-07-25 15:05 554KIndex for binary alignments (bam) file
[   ]Control2h-R1.bedgraph.gz.tbi2017-07-25 15:04 259KBedGraph (wiggle) format file
[   ]Control2h-R2.bedgraph.gz.tbi2017-07-25 15:11 255KBedGraph (wiggle) format file
[   ]BA2h-R2.bedgraph.gz.tbi2017-07-25 15:05 253KBedGraph (wiggle) format file
[   ]BA2h-R1.bedgraph.gz.tbi2017-07-25 15:10 250KBedGraph (wiggle) format file
[   ]BA2h-S1.bedgraph.gz.tbi2017-07-25 15:11 248KBedGraph (wiggle) format file
[   ]Control2h-S1.bedgraph.gz.tbi2017-07-25 15:11 246KBedGraph (wiggle) format file
[   ]BA2h-S2.bedgraph.gz.tbi2017-07-25 15:05 245KBedGraph (wiggle) format file
[   ]Control2h-S2.bedgraph.gz.tbi2017-07-25 15:05 244KBedGraph (wiggle) format file
[   ]BA2h-R3.bedgraph.gz.tbi2017-07-25 15:05 243KBedGraph (wiggle) format file
[   ]Control2h-S3.bedgraph.gz.tbi2017-07-25 15:04 242KBedGraph (wiggle) format file
[   ]Control2h-R3.bedgraph.gz.tbi2017-07-25 15:11 238KBedGraph (wiggle) format file
[   ]BA2h-S3.bedgraph.gz.tbi2017-07-25 15:07 238KBedGraph (wiggle) format file
[   ]BA2h-R2.bed.gz.tbi2017-07-25 15:08 153KTabix index file
[   ]Control2h-R1.bed.gz.tbi2017-07-25 15:05 153KTabix index file
[   ]Control2h-R2.bed.gz.tbi2017-07-25 15:10 153KTabix index file
[   ]BA2h-R1.bed.gz.tbi2017-07-25 15:10 152KTabix index file
[   ]BA2h-S1.bed.gz.tbi2017-07-25 15:08 151KTabix index file
[   ]BA2h-R3.bed.gz.tbi2017-07-25 15:08 150KTabix index file
[   ]Control2h-S1.bed.gz.tbi2017-07-25 15:05 150KTabix index file
[   ]Control2h-S2.bed.gz.tbi2017-07-25 15:08 150KTabix index file
[   ]Control2h-R3.bed.gz.tbi2017-07-25 15:05 150KTabix index file
[   ]BA2h-S2.bed.gz.tbi2017-07-25 15:05 149KTabix index file
[   ]Control2h-S3.bed.gz.tbi2017-07-25 15:04 149KTabix index file
[   ]BA2h-S3.bed.gz.tbi2017-07-25 15:05 148KTabix index file
[   ]Control2h-R1.FJ.bed.gz.tbi2017-07-25 15:05 148KTabix index file
[   ]Control2h-R2.FJ.bed.gz.tbi2017-07-25 15:10 147KTabix index file
[   ]BA2h-R2.FJ.bed.gz.tbi2017-07-25 15:10 147KTabix index file
[   ]BA2h-R1.FJ.bed.gz.tbi2017-07-25 15:08 146KTabix index file
[   ]BA2h-S1.FJ.bed.gz.tbi2017-07-25 15:05 145KTabix index file
[   ]Control2h-S2.FJ.bed.gz.tbi2017-07-25 15:11 144KTabix index file
[   ]Control2h-R3.FJ.bed.gz.tbi2017-07-25 15:11 144KTabix index file
[   ]BA2h-R3.FJ.bed.gz.tbi2017-07-25 15:06 144KTabix index file
[   ]Control2h-S3.FJ.bed.gz.tbi2017-07-25 15:04 144KTabix index file
[   ]Control2h-S1.FJ.bed.gz.tbi2017-07-25 15:07 144KTabix index file
[   ]BA2h-S2.FJ.bed.gz.tbi2017-07-25 15:05 144KTabix index file
[   ]BA2h-S3.FJ.bed.gz.tbi2017-07-25 15:08 142KTabix index file
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