ABI Solid Sequencing

This method should not be confused with "sequencing by synthesis," a principle used by Roche-454 pyrosequencing (introduced in 2005, generating millions of 200-400bp reads in 2009), and the Solexa system (now owned by Illumina) (introduced in 2006, generating hundreds of millions of 50-100bp reads in 2009) These methods have reduced the cost from $0.01/base in 2004 to nearly $0.0001/base in 2006 and increased the sequencing capacity from 1,000,000 bases/machine/day in 2004 to more than 5,000,000,000 bases/machine/day in 2009.

Over 30 publications exist describing its use first for nucleosome positioning from Valouev et al.,[1] transcriptional profiling or strand sensitive RNA-Seq with Cloonan et al.,[2] single cell transcriptional profiling with Tang et al.[3] and ultimately human resequencing with McKernan et al.[4] The method used by this machine (sequencing-by-ligation) has been reported to have some issue sequencing palindromic sequences.

Microarrays was once the mainstay of the transcriptomics the last ten years and array based technology has subsequently branched out to other areas.

Any organism's entire transcriptome could be potentially sequenced in one run (for very small bacterial genomes) and not only would the identification of each transcript be available but expression profiling is possible as quantitative reads can also be achieved.

Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein interactions.

The ability to learn more about methylation and TF binding sites on a genome wide scale is a valuable resource and could teach us much about disease and molecular biology in general.