Gene expression profiling of the Arabidopsis Mediator MED5 mutant ref4-3 and suppressors thereof

Purpose: To identify changes in gene expression in the ref4-3 mutant that contribute to the mutant's altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and suppressors of ref4-3. Methods: Gene expression profiles were generated from 18-day-old, pooled Arabidopsis rosettes in biological quadruplicate, by paired-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR. Results: We identified 14,688 genes that were differentially expressed across the 10 genotypes (ANOVA, FDR <0.05). Overall design: Gene expression profiles of wild type and Mediator single or double mutants were generated in biological quadruplicate from 18-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.