iPlant Collaborator: RNAseq Analysis in the Discovery Environment

Plant organs use gravity as a growth guide, a process called gravitropism. Accordingly, shoots grow upward toward light, which they can use for photosynthesis, and roots grow downward, into the soil, when they can take up water and nutrients needed for plant growth and development, as well as anchor the plant. A better understanding of the genetic networks that govern these responses will give us important insights into the molecular and cellular processes involved. We are using RNAseq to analyse the transcriptomic response of the Arabidopsis thaliana root tip to alterations in their orientation relative to the gravity vector. Four time points were chosen: 0, 5, 20 and 150 minutes after stimulation, to assess the genetic basis of key molecular and cellular responses that lead to alterations in growth orientation under these conditions. Samples were multiplexed and sequenced on an Illumina HiSEQ2000 machine. A single paired end cDNA library was sequenced for each time point, constituting approximately 90 million 100 bp fragments that were investigated to uncover alternative-splicing and other transcriptional-variant isoforms. To investigate differential gene expression throughout the time course cDNA libraries generated from three biological repeats were sequenced and mapped to the TAIR10 Arabidopsis genome using the using Tuxedo applications in the iPlant Discovery Environment. In addition, small RNA (sRNA) libraries were also generated, sequenced and then investigated using the UEA small RNA work bench to explore the contribution of miRNAs and siRNAs in the gravitropic response using the iPlant Atmosphere cloud-computing platform.