Whole Genome Analysis Using Microarrays

Abstract

The development of microarray technology has allowed the genomes of mycobacteria to be directly compared to identify DNA regions that differ between strains due to deletion, insertion, or sequence divergence. The use of microarrays in comparative genomics has proved to be a valuable tool for comparing both mycobacterial species and strains. We describe here the methodology for comparing two mycobacterial DNA samples by microarray hybridization, from labeling and slide preparation, to DNA microarray analysis options. Further developments in microarray design and methodology promise to ensure that microarrays remain an important resource for comparative genomic studies in the future.

Contrasting Transcriptional Responses of a Virulent and an Attenuated Strain of Mycobacterium tuberculosis Infecting Macrophages

“…Genomic DNA was extracted from the bacteria using previously published protocols by Belisle et al [31] . Two micrograms each of Mtb H37Ra and H37Rv genomic DNA were hybridized to TBv2.1.1 M. tuberculosis complex whole genome microarray, generated by the Bacterial Microarray Group at St. George's, as previously described [32] DNA extracted from two biological replicates were hybridized in duplicate. The array design is available in BμG@Sbase (accession number: A-BUGS-23; http://bugs.sgul.ac.uk/A-BUGS-23 ) and also ArrayExpress (accession number: A-BUGS-23).…”

“… [33] , from both axenic broth cultures of bacteria as well as intracellular bacteria at day 7 post-infection. Microarray hybridizations were conducted as previously described [32] with 4 µg Cy5-labelled cDNA derived from either H37Rv or H37Ra RNA hybridized against 2 µg Cy3-labelled M. tuberculosis H37Rv genomic DNA. RNA extracted from three biological replicates of each strain were hybridized in duplicate.…”