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


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.

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Figure 1: Scheme of SuperSAGE array.
Figure 2: SuperSAGE array analysis of leaves and suspension-cultured cells of rice.
Figure 3: Gene expression profiles in NbCD1- or NbCD3-overexpressing N. benthamiana leaves as revealed by SuperSAGE array.
Figure 4: Isolation of full-length cDNAs of the genes corresponding to SuperSAGE tags by RACE in N. benthamiana.

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Gene Expression Omnibus


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We dedicate this work to late H. Enei, the former director of Iwate Biotechnology Research Center, who strongly encouraged our study. We are grateful to Genefrontier Corp. and NimbleGen Systems Inc. for constructing and analyzing oligonucleotide arrays. This study was supported in part by a grant from the Program for Promotion of Basic Research Activities for Innovative Biosciences (Japan). Work in Berlin was supported by Deutsche Forschungsgemainshaft (KR1293/4-1).

Author information




H.M. contributed to development and implementation of the core technique, K.H.B.N. contributed to NbCD1 and NbCD3 experiments, K.Y. contributed to rice experiments, A.I. contributed to NbCD1 and NbCD3 experiments, and G.K., D.H.K. and R.T. contributed to development of the core technique.

Corresponding author

Correspondence to Hideo Matsumura.

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Competing interests

G.K. is employed by GenXPro.

Supplementary information

Supplementary Fig. 1

Reproducibility of SuperSAGE-Array analysis in leaves and suspension-cultured cells of rice. (PDF 997 kb)

Supplementary Table 1

List of rice SuperSAGE tags spotted on the oligonucleotide array and averaged hybridization signal values in rice leaves and suspension-cultured cells. (PDF 151 kb)

Supplementary Table 2

SuperSAGE tags of genes differentially regulated by NbCD1-overexpression in N. benthamiana leaves. (PDF 94 kb)

Supplementary Table 3

SuperSAGE tags of genes differentially regulated by NbCD3-overexpression in N. benthamiana leaves. (PDF 91 kb)

Supplementary Table 4

Average of normalized hybridization signal values (Log2) of differentially expressed genes between GFP- and NbCD1-overexpressing N. benthamiana leaves. (PDF 113 kb)

Supplementary Table 5

Average of normalized hybridization signal values (Log2) of differentially expressed genes between GFP- and NbCD3-overexpressing N. benthamiana leaves. (PDF 115 kb)

Supplementary Table 6

Summary of genes isolated by RACE PCR. (PDF 47 kb)

Supplementary Methods (DOC 26 kb)

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Matsumura, H., Bin Nasir, K., Yoshida, K. et al. SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods 3, 469–474 (2006).

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