SuperSAGE is a derivative of SAGE that uses the type III-endonuclease EcoP15I of phage P1, to cut 26 bp long sequence tags from each transcript's cDNA, expanding the tag-size by at least 6 bp as compared to the predecessor techniques SAGE and LongSAGE. The longer tag-size allows for a more precise allocation of the tag to the corresponding transcript, because each additional base increases the precision of the annotation considerably.
Like in the original SAGE protocol, so-called ditags are formed, using blunt-ended tags. However, SuperSAGE avoids the bias observed during the less random LongSAGE 20 bp ditag-ligation. By direct sequencing with high-throughput sequencing techniques (next-generation sequencing, i.e. pyrosequencing), hundred thousands or millions of tags can be analyzed simultaneously, producing very precise and quantitative gene expression profiles. Therefore, tag-based gene expression profiling also called "digital gene expression profiling" (DGE) can today provide most accurate transcription profiles that overcome the limitations of microarrays.