Purpose: To identify changes in gene expression in ref4-3 mutant that contribute to the mutant's altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and ref4-3 cdk8-1. Methods: Gene expression profiles were generated from 20-day-old, pooled Arabidopsis rosettes in biological triplicate, by paried-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 7,355 genes that were differentially expressed in ref4-3 compared to wild type, part of which were significantly rescued by loss of CDK8 (FDR <0.05). Overall design: Gene expression profiles of wild type and Mediator single or double mutants were generated in biological triplicate from 20-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.