ARTRA: A new database of the Arabidopsis transcriptome and gene-specific sequences for microarray probes and RNAi triggers

Abstract

A new Arabidopsis transcriptome and microarray (ARTRA) database has been developed that contains transcriptome sequences and gene-specific sequences for a DNA microarray and RNAi knockdown triggers. Probes for the microarray were developed using sequences from the ARTRA database are characterized by long gene-specific fragments and spotting as a single sense strand. As a result, the gene-specificity and sensitivity of this microarray were both high, and therefore the ratio of gene expression from the present array was highly correlated with that from the Affymetrix GeneChip (R2 = 0.95). Moreover, AGAMOUS gene expression was reduced to about 10% of wild-type in Tl plants transformed with a vector containing an inverted repeat of the gene-specific fragment of AGAMOUS. Flowers of the Tl plants lacked pistils and stamens, which is the phenotype of known AGAMOUS knockout plants. This result showed that gene knockdown is possible in transgenic plants with the inverted repeat structure using a gene-specific fragment. RNAi knockdown is important as an approach for genes without T-DNA tag lines. Access to the ARTRA database is available to any researcher on request from the web site of htt://artra.kazusa. or.jp/.