title: A new microarray platform for whole-genome expression profiling of Mycobacterium tuberculosis.
abstract: 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.
authors.affiliation: Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
authors.forename: Balaji
authors.initials: B
authors.lastname: Venkataraman
authors.affiliation: Bionivid Technology [P] Ltd, 401-4 AB Cross, 1st Main, Kasturi Nagar, East of NGEF, Bangalore 560043, India.
authors.forename: Madavan
authors.initials: M
authors.lastname: Vasudevan
authors.affiliation: Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India. Electronic address: amitagupta@south.du.ac.in.
authors.forename: Amita
authors.initials: A
authors.lastname: Gupta
mesh_terms: D020869:Gene Expression Profiling / Q000295:instrumentation*; D016680:Genome, Bacterial / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D025341:Principal Component Analysis; D015203:Reproducibility of Results
keywords: M. tuberculosis; Microarray; RNA amplification; Whole genome expression profiling