RNA-Seq analysis comparing gene expression changes between Col-0 wild-type (WT) and sig2-2 mutant lines at the whole genome level

To understand the transcriptional role of SIGMA FACTOR 2 (SIG2) in Red (R) light-dependent growth and development, RNA-sequencing analysis was perfomed to compare gene expression in a sig2-2 mutant and Col-0 wild-type seedlings grown in R light at two developmental stages (1-day and 7-day). Overall design: Total RNA was isolated from 1- or 7-d-old whole seedlings of Col-0 WT and sig2-2 mutant lines, grown in Red-light with three biological replicates. Sequencing samples were prepared using the Illumina TruSeq mRNA prep kit, and RNA-seq was performed by the Research Technology Support Facility at Michigan State University using the Illumina sequencing system.