RNA-Seq expression profiling of srta mutant and WT strains of Chlamydomonas reinhardtii

Two strains of the green alga, Chlamydomonas reinhardtii, were selected for high expression of transgenes. These strains, called UVM4 and UVM11, were found to both have unique mutations in the SRTA gene (Cre10.g462200). In this study, the basal transcriptome of these two strains was compared to that of their WT parental strain, Elow47, to identify what effects, if any, the srta mutation has on the transcriptome. Additionally, two SRTA complemented strains in a UVM11 background (UVM11-C1 and UVM11-C9) were included for comparison. Overall design: Two different srta mutant strains (UVM4 and UVM11), the SRTA WT parental strain (Elow47), and two SRTA complemented strains (UVM11-C1 and UVM11-C9) were used for an RNA-Seq analysis to identify differentially expressed genes. The analysis was conducted in two batches. In batch 1, RNA was purified and analyzed from four separate cultures of UVM4, UVM11, and Elow47. In batch 2, RNA was purified and analyzed from three separate cultures of UVM11 (repeated to identify batch effects), UVM11-C1, and UVM11-C9.