Illumina sequencing

We are using the Illumina (Solexa) high-throughput sequencing platform to sequence whole microbial genomes and transcriptomes. This technology generates millions of 36bp reads per run, reaching over a giga base of sequence in just a few days. The Illumina technology enables us to study the evolution of bacteria, discover phenotype altering mutations, and document dynamic evolutionary processes.

We are also sequencing cDNAs of bacteria growing in different conditions, and measuring differential expression. This "digital microarray" technology is more accurate and gives a higher resolution than the commonly used microarrays.

Our lab uses the Illumina technoogy to discover new small non-coding RNAs (sRNAs) and understand their biological functions. It is gradually becoming clear that microbial genomes are populated by functional sRNAs, generally 50-500bp long. These sRNAs have been shown to regulate various biological processes including quorum sensing, pathogenesis, stress response, and more. While ~80 sRNAs were characterized in E. coli through extensive studies, very little is known on sRNAs in other prokaryotes. By sequencing the transcriptomes of various bacteria and archaea, we detect intergenic regions that are expressed and thereby find new sRNAs.

At right: The Illumina HiSeq 2000 at the Weizmann Institute of Science