The Solexa Genome Analysis System provides DNA sequencing, expression profiling and micro-RNA analysis and is comprised of the 1G Genetic Analyzer, the Cluster Station, and associated reagents, consumables, and software. The system can generate over a billion bases of sequence per run. The system is intended to enable researchers to generate economical sequence-based digital readout of transcript abundance by assessing up to 5 million transcript tags per sample at costs comparable to those of hybridization arrays.