Strep Array Project

Group A Streptococci Microarray Project

Rationale: The human upper respiratory tract is the only known reservoir for group A streptococci, and adherence to pharyngeal epithelial cells is the first overt step in establishing infection. Bacterial-host interactions are dynamic processes, and as streptococci enter the pharyngeal cell environment, they process and respond to environmental cues, which directly or indirectly regulate the expression of genes involved in adherence and internalization. A global understanding of transcriptional responses of streptococci during adherence and other stages of infection would help to elucidate the molecular events that occur during this initial infection stage.

Approach: We developed and used spotted oligonucleotide microarrays of the genomes of Streptococcus pyogenes strains SF370 (M1 serotype) and MGAS8232 (M18 serotype) to study genome wide expression profiles of streptococci during various stages of infection or under various culture conditions.

Microarrays: We have designed and used spotted oligonucleotide microarrays that represent every unique open reading frame for all Streptococcus pyogenes genomes sequenced as of January 2008.

Data and Software: Available for download are the raw intensity and processed data from a statistics-based evaluation of differential gene expression of strain SF370 during adherence to cultured human pharyngeal epithelial cells as compared to non-adherent ("associated") streptococci within the same experiment. The resulting data from each processing step are presented. GenomeCrawler, an algorithm with dynamic windowing that we developed to identify clusters of functionally related gene neighbors from the processed microarray data, and an application called GenomeSpyer for visualization of the GenomeCrawler output are available for download under the software link below.

Software (Note: In order to run the following downloaded software, the program R, available at http://www.R-project.org, must first be downloaded and installed on your operating system.)
    Download Software.tar.gz (gzipped file for UNIX platform)
    Download Software.zip (Zip file for Windows PC)

Data
    Download Data.tar.gz (tar.gz file for UNIX platform)
    Download Data.zip (Zip file for Windows PC)

Supplementary Tables
    Supplementary Table 1 (Microsoft Excel file)
    Supplementary Table 2 (Microsoft Excel file)
    Supplementary Table 3 (Microsoft Excel file)

For permission to access data and software downloads, please contact Patricia Ryan.