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:
- BA2h-R1 - BA-treated roots, replicate 1
- BA2h-R2 - BA-treated roots, replicate 2
- BA2h-R3 - BA-treated roots, replicate 3
- BA2h-S1 - BA-treated shoots, replicate 1
- BA2h-S2 - BA-treated shoots, replicate 2
- BA2h-S3 - BA-treated shoots, replicate 3
- Control2h-R1 - mock-treated roots, replicate 1
- Control2h-R2 - mock-treated roots, replicate 2
- Control2h-R3 - mock-treated roots, replicate 3
- Control2h-S1 - mock-treated shoots, replicate 1
- Control2h-S2 - mock-treated shoots, replicate 2
- Control2h-S3 - mock-treated shoots, replicate 3
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.
Name | Last modified | Size | Description | |
---|---|---|---|---|
Parent Directory | - | |||
Control2h-R1.bam | 2017-07-25 15:05 | 3.2G | Binary alignments file | |
Control2h-R2.bam | 2017-07-25 15:11 | 3.0G | Binary alignments file | |
BA2h-R1.bam | 2017-07-25 15:07 | 2.9G | Binary alignments file | |
BA2h-S1.bam | 2017-07-25 15:10 | 2.7G | Binary alignments file | |
BA2h-R2.bam | 2017-07-25 15:09 | 2.7G | Binary alignments file | |
BA2h-S2.bam | 2017-07-25 15:08 | 2.5G | Binary alignments file | |
Control2h-S2.bam | 2017-07-25 15:05 | 2.4G | Binary alignments file | |
Control2h-S1.bam | 2017-07-25 15:06 | 2.4G | Binary alignments file | |
Control2h-S3.bam | 2017-07-25 15:10 | 2.2G | Binary alignments file | |
BA2h-R3.bam | 2017-07-25 15:08 | 2.1G | Binary alignments file | |
Control2h-R3.bam | 2017-07-25 15:06 | 2.0G | Binary alignments file | |
BA2h-S3.bam | 2017-07-25 15:09 | 1.9G | Binary alignments file | |
Control2h-R1.bedgraph.gz | 2017-07-25 15:04 | 134M | BedGraph (wiggle) format file | |
Control2h-R2.bedgraph.gz | 2017-07-25 15:07 | 127M | BedGraph (wiggle) format file | |
BA2h-R1.bedgraph.gz | 2017-07-25 15:05 | 123M | BedGraph (wiggle) format file | |
BA2h-R2.bedgraph.gz | 2017-07-25 15:06 | 119M | BedGraph (wiggle) format file | |
BA2h-S1.bedgraph.gz | 2017-07-25 15:07 | 114M | BedGraph (wiggle) format file | |
Control2h-S2.bedgraph.gz | 2017-07-25 15:08 | 108M | BedGraph (wiggle) format file | |
BA2h-S2.bedgraph.gz | 2017-07-25 15:10 | 108M | BedGraph (wiggle) format file | |
Control2h-S1.bedgraph.gz | 2017-07-25 15:07 | 108M | BedGraph (wiggle) format file | |
Control2h-S3.bedgraph.gz | 2017-07-25 15:10 | 108M | BedGraph (wiggle) format file | |
BA2h-R3.bedgraph.gz | 2017-07-25 15:06 | 106M | BedGraph (wiggle) format file | |
Control2h-R3.bedgraph.gz | 2017-07-25 15:10 | 106M | BedGraph (wiggle) format file | |
BA2h-S3.bedgraph.gz | 2017-07-25 15:10 | 99M | BedGraph (wiggle) format file | |
Control2h-R1.bed.gz | 2017-07-25 15:05 | 3.0M | Annotation or junction file | |
Control2h-R2.bed.gz | 2017-07-25 15:08 | 3.0M | Annotation or junction file | |
BA2h-R2.bed.gz | 2017-07-25 15:08 | 2.9M | Annotation or junction file | |
BA2h-R1.bed.gz | 2017-07-25 15:10 | 2.9M | Annotation or junction file | |
BA2h-S1.bed.gz | 2017-07-25 15:05 | 2.9M | Annotation or junction file | |
BA2h-S2.bed.gz | 2017-07-25 15:08 | 2.8M | Annotation or junction file | |
Control2h-S1.bed.gz | 2017-07-25 15:04 | 2.8M | Annotation or junction file | |
Control2h-S2.bed.gz | 2017-07-25 15:10 | 2.8M | Annotation or junction file | |
Control2h-S3.bed.gz | 2017-07-25 15:05 | 2.8M | Annotation or junction file | |
Control2h-R3.bed.gz | 2017-07-25 15:08 | 2.8M | Annotation or junction file | |
BA2h-R3.bed.gz | 2017-07-25 15:09 | 2.8M | Annotation or junction file | |
BA2h-S3.bed.gz | 2017-07-25 15:08 | 2.7M | Annotation or junction file | |
Control2h-R1.FJ.bed.gz | 2017-07-25 15:05 | 2.6M | Loraine Lab FindJunctions file | |
Control2h-R2.FJ.bed.gz | 2017-07-25 15:10 | 2.6M | Loraine Lab FindJunctions file | |
BA2h-R2.FJ.bed.gz | 2017-07-25 15:11 | 2.5M | Loraine Lab FindJunctions file | |
BA2h-R1.FJ.bed.gz | 2017-07-25 15:08 | 2.5M | Loraine Lab FindJunctions file | |
BA2h-S1.FJ.bed.gz | 2017-07-25 15:08 | 2.5M | Loraine Lab FindJunctions file | |
Control2h-S1.FJ.bed.gz | 2017-07-25 15:10 | 2.5M | Loraine Lab FindJunctions file | |
BA2h-S2.FJ.bed.gz | 2017-07-25 15:08 | 2.5M | Loraine Lab FindJunctions file | |
Control2h-S2.FJ.bed.gz | 2017-07-25 15:06 | 2.5M | Loraine Lab FindJunctions file | |
Control2h-S3.FJ.bed.gz | 2017-07-25 15:04 | 2.5M | Loraine Lab FindJunctions file | |
Control2h-R3.FJ.bed.gz | 2017-07-25 15:06 | 2.4M | Loraine Lab FindJunctions file | |
BA2h-R3.FJ.bed.gz | 2017-07-25 15:07 | 2.4M | Loraine Lab FindJunctions file | |
BA2h-S3.FJ.bed.gz | 2017-07-25 15:08 | 2.4M | Loraine Lab FindJunctions file | |
Control2h-R1.bam.bai | 2017-07-25 15:08 | 633K | Index for binary alignments (bam) file | |
Control2h-R2.bam.bai | 2017-07-25 15:06 | 625K | Index for binary alignments (bam) file | |
BA2h-R1.bam.bai | 2017-07-25 15:10 | 618K | Index for binary alignments (bam) file | |
BA2h-R2.bam.bai | 2017-07-25 15:08 | 612K | Index for binary alignments (bam) file | |
BA2h-S1.bam.bai | 2017-07-25 15:10 | 597K | Index for binary alignments (bam) file | |
BA2h-S2.bam.bai | 2017-07-25 15:08 | 586K | Index for binary alignments (bam) file | |
Control2h-S2.bam.bai | 2017-07-25 15:08 | 585K | Index for binary alignments (bam) file | |
Control2h-S1.bam.bai | 2017-07-25 15:06 | 582K | Index for binary alignments (bam) file | |
Control2h-R3.bam.bai | 2017-07-25 15:08 | 571K | Index for binary alignments (bam) file | |
BA2h-R3.bam.bai | 2017-07-25 15:04 | 570K | Index for binary alignments (bam) file | |
Control2h-S3.bam.bai | 2017-07-25 15:04 | 567K | Index for binary alignments (bam) file | |
BA2h-S3.bam.bai | 2017-07-25 15:05 | 554K | Index for binary alignments (bam) file | |
Control2h-R1.bedgraph.gz.tbi | 2017-07-25 15:04 | 259K | BedGraph (wiggle) format file | |
Control2h-R2.bedgraph.gz.tbi | 2017-07-25 15:11 | 255K | BedGraph (wiggle) format file | |
BA2h-R2.bedgraph.gz.tbi | 2017-07-25 15:05 | 253K | BedGraph (wiggle) format file | |
BA2h-R1.bedgraph.gz.tbi | 2017-07-25 15:10 | 250K | BedGraph (wiggle) format file | |
BA2h-S1.bedgraph.gz.tbi | 2017-07-25 15:11 | 248K | BedGraph (wiggle) format file | |
Control2h-S1.bedgraph.gz.tbi | 2017-07-25 15:11 | 246K | BedGraph (wiggle) format file | |
BA2h-S2.bedgraph.gz.tbi | 2017-07-25 15:05 | 245K | BedGraph (wiggle) format file | |
Control2h-S2.bedgraph.gz.tbi | 2017-07-25 15:05 | 244K | BedGraph (wiggle) format file | |
BA2h-R3.bedgraph.gz.tbi | 2017-07-25 15:05 | 243K | BedGraph (wiggle) format file | |
Control2h-S3.bedgraph.gz.tbi | 2017-07-25 15:04 | 242K | BedGraph (wiggle) format file | |
Control2h-R3.bedgraph.gz.tbi | 2017-07-25 15:11 | 238K | BedGraph (wiggle) format file | |
BA2h-S3.bedgraph.gz.tbi | 2017-07-25 15:07 | 238K | BedGraph (wiggle) format file | |
BA2h-R2.bed.gz.tbi | 2017-07-25 15:08 | 153K | Tabix index file | |
Control2h-R1.bed.gz.tbi | 2017-07-25 15:05 | 153K | Tabix index file | |
Control2h-R2.bed.gz.tbi | 2017-07-25 15:10 | 153K | Tabix index file | |
BA2h-R1.bed.gz.tbi | 2017-07-25 15:10 | 152K | Tabix index file | |
BA2h-S1.bed.gz.tbi | 2017-07-25 15:08 | 151K | Tabix index file | |
BA2h-R3.bed.gz.tbi | 2017-07-25 15:08 | 150K | Tabix index file | |
Control2h-S1.bed.gz.tbi | 2017-07-25 15:05 | 150K | Tabix index file | |
Control2h-S2.bed.gz.tbi | 2017-07-25 15:08 | 150K | Tabix index file | |
Control2h-R3.bed.gz.tbi | 2017-07-25 15:05 | 150K | Tabix index file | |
BA2h-S2.bed.gz.tbi | 2017-07-25 15:05 | 149K | Tabix index file | |
Control2h-S3.bed.gz.tbi | 2017-07-25 15:04 | 149K | Tabix index file | |
BA2h-S3.bed.gz.tbi | 2017-07-25 15:05 | 148K | Tabix index file | |
Control2h-R1.FJ.bed.gz.tbi | 2017-07-25 15:05 | 148K | Tabix index file | |
Control2h-R2.FJ.bed.gz.tbi | 2017-07-25 15:10 | 147K | Tabix index file | |
BA2h-R2.FJ.bed.gz.tbi | 2017-07-25 15:10 | 147K | Tabix index file | |
BA2h-R1.FJ.bed.gz.tbi | 2017-07-25 15:08 | 146K | Tabix index file | |
BA2h-S1.FJ.bed.gz.tbi | 2017-07-25 15:05 | 145K | Tabix index file | |
Control2h-S2.FJ.bed.gz.tbi | 2017-07-25 15:11 | 144K | Tabix index file | |
Control2h-R3.FJ.bed.gz.tbi | 2017-07-25 15:11 | 144K | Tabix index file | |
BA2h-R3.FJ.bed.gz.tbi | 2017-07-25 15:06 | 144K | Tabix index file | |
Control2h-S3.FJ.bed.gz.tbi | 2017-07-25 15:04 | 144K | Tabix index file | |
Control2h-S1.FJ.bed.gz.tbi | 2017-07-25 15:07 | 144K | Tabix index file | |
BA2h-S2.FJ.bed.gz.tbi | 2017-07-25 15:05 | 144K | Tabix index file | |
BA2h-S3.FJ.bed.gz.tbi | 2017-07-25 15:08 | 142K | Tabix index file |