Global gene expression in Moraxella catarrhalis ATCC43617 cells grown in the planktonic and in biofilm states

Total RNA samples were isolated from M. catarrhalis grown in the planktonic state (i.e., in broth) and in a biofilm. Biofilms were generated by growing this strain in the continuous-flow Sorbarod filter system for three days. Total RNA samples and M. catarrhalis genome-directed primers (GDPs) were used for synthesis of Cy3- or Cy5-labeled cDNA samples. Five independent M. catarrhalis growth experiments and total RNA isolations were used for the synthesis of cDNA samples, and a total of six DNA microarray hybridizations were performed in this study. Keywords: Effect of Growth Environment on Global Gene Expression by Moraxella catarrhalis The Moraxella catarrhalis DNA microarray was constructed based on the nucleotide sequence of the genome of M. catarrhalis strain ATCC 43617. The ORFs in the genome were identified by using GLIMMER 2.02. The 1,761 annotated ORFs were used to design 70-mer oligonucleotides that would specifically anneal to each ORF. Because genome-directed primers that annealed within the 3' 30% of each ORF were used to synthesize cDNA, each 70-mer probe was designed to anneal to a region within the 5' 70% of each ORF.