SuperSAGE: A Modern Platform for Genome-Wide Quantitative Transcript Profiling

Hideo      Matsumura; Detlev   H.   Kruger; Gunter      Kahl; Ryohei      Terauchi

Abstract

SuperSAGE is a variant of SAGE (Serial Analysis of Gene Expression) technology, which allows making transcript profiling by 26-bp tags extracted from cDNA employing the typeIII restriction enzyme EcoP15I. Its tag length is the longest among all the versions of SAGE, and is advantageous in tag-to-gene annotation, thereby allowing the technique to applicable to any eukaryotic life organisms. For model organisms with genome or cDNA sequences available, genes corresponding to 26-bp tags are uniquely defined by simple BLAST search. For non-model organisms without these sequence information, the 26-bp tag sequence is directly applicable to design PCR primer for amplifying cDNA of corresponding genes by 3- or 5-RACE. Furthermore, SuperSAGE allows various applications including “interaction transcriptome” and “SuperSAGE array”. Emerging “Next Generation Sequencing” technologies perfectly complement Super- SAGE, and their combination has generated a novel transcriptome platform, that is superior to all the different microarray variants in terms of throughput, data quality and cost of analysis.

Keywords: Transcriptome, SuperSAGE, non-model organism, interaction transcriptome, SuperSAGE array, Next Generation Sequencing, microarray

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