SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays

Nat Methods. 2006 Jun;3(6):469-74. doi: 10.1038/nmeth882.


We developed a new platform for genome-wide gene expression analysis in any eukaryotic organism, which we called SuperSAGE array. The SuperSAGE array is a microarray onto which 26-bp oligonucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. We demonstrated highly reproducible gene expression profiling by the SuperSAGE array for 1,000 genes (tags) in rice. We also applied this technology to the detailed study of expressed genes identified by SuperSAGE in Nicotiana benthamiana, an organism for which sufficient genome sequence information is not available. We propose that the SuperSAGE array system represents a new paradigm for microarray construction, as no genomic or cDNA sequence data are required for its preparation.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing / genetics
  • Equipment Design
  • Equipment Failure Analysis
  • Expressed Sequence Tags*
  • Gene Expression Profiling / instrumentation*
  • Gene Expression Profiling / methods
  • Oligonucleotide Array Sequence Analysis / instrumentation*
  • Oligonucleotide Array Sequence Analysis / methods
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Transcription Factors / genetics*


  • Transcription Factors