Biofilms of non-tuberculous mycobacteria display distinct expression patterns and form an extracellular matrix

Comparison of transcriptional differences (RNA-seq) between biofilm and planktonic cultures of Mycobacterium chelonae For pellicle samples, cultures of Mycobacterium chelonae were grown in 75cm2 cap-vented culture flasks in a 30 degrees C static incubator for 5 (t1) or 10 (t2) days. For planktonic samples, M. chelonae was cultured in the same way as pellicle samples, but tyloxapol was added to a final concentration of 0.05%. Samples were collected from pellicle and planktonic cultures from four independent experiments. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.