A new microarray platform for whole-genome expression profiling of Mycobacterium tuberculosis

• An in situ synthesized oligonucleotide microarray for M. tuberculosis is described.
• This updated microarray design is a more complete representation of the genome.
• RNA amplification, preparation of labeled target and hybridization have been optimized.
• This validated microarray allows for accurate gene expression profiling of M. tuberculosis.

Microarrays have allowed gene expression profiling to progress from the gene level to the genome level, and oligonucleotide microarrays have become the platform of choice for large-scale, targeted gene expression studies. cDNA arrays and spotted oligonucleotide arrays have gradually given way to in situ synthesized oligonucleotide-based DNA microarrays for whole-genome expression profiling. With the identification of new coding and regulatory sequences, it is imperative that microarrays be updated to enable more complete expression profiling of genomes. We report here a new in situ synthesized oligonucleotide-based microarray platform for Mycobacterium tuberculosis that has been updated for the latest genome information and incorporates hitherto unannotated genes with described biological functions. This microarray has greater coverage of mycobacterial genes than any other array reported to date. We have also evaluated different labeled-target preparation methods and hybridization conditions for this new microarray to obtain high quality data and reproducible results. The new design has been rigorously validated for its specificity and performance using samples isolated from mycobacteria grown under different environment conditions. Further, the quality of the generated data has been compared with published data and is superior to that obtained using spotted oligonucleotide microarrays.