Purpose: To identify changes in gene expression in ref5-1 and ref2-1 compared with wild type and ref5-1 med5 and ref2-1 med5 compared to ref5-1 or ref2-1 respectively 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 71 genes that were differentially expressed in both ref5-1 and ref2-1 compared to wild type but their altered expression is restored. Overall design: Gene expression profiles of wild type and mutants were generated in biological triplicate from 18-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.