RNA-Seq Data

This page contains the RNA-Seq results for all of the wildtype and transgenic trees generated in this project. We used TruSeq RNA sample preparation kit (Illumina, San Diego, CA), and the samples were pooled for multiplex sequencing and ran on the Illumina GAIIx platform. The resulting FASTQ files from the Illumina GAIIx were mapped onto the genome of P. trichocarpa version 3.0 using Bowtie and Tophat. BAM (Binary Sequence Alignment / Map) files were converted to raw counts using BedTool. Then a normalized count was obtained using the Trimmed Means of M value (TMM). To view the RNA-Seq results, enter the transgenic line identifies (separated by spaces of commas) into the space bar below, and click display data. Alternatively, specific RNA-Seq data could be downloaded by clicking on the “RNA Seq Download” link. The raw reads will be deposited into a public RNA-Seq database during 2016. If you have any questions about these data, would like to use these data for publication, or would like to collaborate, please contact Vincent Chiang (Contacts Page).

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Enter a list of transgenic line ids to get a table of the normalized count values for those lines (for genes being investigated in this project).