Transcriptomic Analysis of Rhodobacter sphaeroides

RNA was isolated from exponential phase cultures of R. sphaeroides strains that were grown photosynthetically in 16 mL screw cap tubes or 500 ml cultures in roux bottles with bubbling (95% N₂, 5% CO₂) [11] (link),[78] (link). RNA isolation and subsequent cDNA synthesis, labeling and hybridization to R. sphaeroides GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described [82] (link). Microarray datasets were normalized by Robust Multichip Average (RMA) to log₂ scale with background adjustment and quantile normalization [83] (link). Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package [84] . Correction for multiple testing was done using Benjamini-Hochberg correction [85] . All analyses were conducted in the R statistical programming environment (http://www.R-project.org).