Custom microarray design based on RNA-Seq data

Microarray technology is a powerful tool for studying genome-wide gene expression. As the genome of many fish has not yet been determined, however, cDNA microarrays can only be designed from limited known sequence data.

In this study, researchers at Tokyo University of Marine Science and Technology, Japan designed a microarray based on the sequencing data (337,466 reads) obtained by next-generation sequencing of RNA extracted from rainbow trout (Oncorhynchus mykiss) embryonic genital ridge, testis, and ovary.

These data (307,264 reads) were assembled into 28,668 contigs. Based on this information, 55,928 microarray probes were designed for a microarray, which was validated by hybridizing experiments with RNA extracted from type A spermatogonia (A-SG) and testicular somatic cells. The rainbow trout gonad microarray developed in this study therefore appears to be a useful tool to understand gametogenesis in rainbow trout.

  • Hayashi M, Sato M, Iwasaki Y, Terasawa M, Tashiro M, Yokoyama S, Katayama N, Sadaie S, Miwa M, Yoshizaki G. (2012) Combining next-generation sequencing with microarrays for transcriptome analysis in rainbow trout gonads. Mol Reprod Dev [Epub ahead of print]. [abstract]