SuperSAGE advice

IWATE, Japan—Looking to combine the throughput of microarrays with the "open" nature of serial analysis of gene expression (SAGE), researchers at GenXPro GmbH and several Japanese and German research institutes developed a new assay system they call SuperSAGE array.

In proof-of-concept work, published in Nature Methods, the scientists tested the system against a well characterized genome and one more poorly elucidated.

The researchers generated a 1000-tag library of the rice genome and used NimbleGen Systems on-chip synthesis to generate an equivalent array. They then examined expression profiles of leaf and cultured-cell RNA, finding good agreement both between the two techniques and with published data.

The scientists then repeated the experiment with the more poorly characterized genome of Nicotiana benthamiana. They could clearly monitor and quantify gene expression changes controlled by proteins involved in cell death, and identified several genes involved in this process using cDNA amplification. The researchers therefore suggest that the combined SuperSAGE/array approach opens the door to gene expression studies in non-model species with poorly characterized genomes.