Transcriptome comparison of S. pyogenes strains MGAS2221 and 2221ΔrivRX

The rivR gene encodes a putative transcriptional regulator, while the rivX gene encodes a putative small regulatory RNA. To determine the RivRX regulon during exponential phase growth in THY broth we compared parental strain MGAS2221 with isogenic rivRX mutant strain 2221ΔrivRX. GAS strains were grown in THY broth to mid-exponential phase, corresponding to an O.D.600 of 0.5. A 4.5ml aliquot of each GAS culture was added to 9ml of RNAprotect (Qiagen Inc.). Following addition of RNAprotect, samples were incubated at room temperature for 5 mins before centrifuging. Supernatant was removed and the pellets quick frozen in liquid nitrogen and stored at -80 °C until ready to use. RNA isolation, cDNA synthesis, and use of our custom Affymetrix microarray was as previously described (Perez et al., 2009)