Transcriptomics

Dataset Information

43

Expression profile in response to salt-treatment in wheat using 22k microarray


ABSTRACT: Analysis of transcripts in response to salt treatment. In order to design the 22k wheat oligo-DNA microarray, a total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multi-step selection of the sense strand, 21,939 60-mer oligo DNA probes were selected for attachment on the microarray slide. This 22k oligo DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than two-fold in response to salt. These included genes known to mediate the response to salt as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription (RT)-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in the response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo DNA microarray is a reliable method for monitoring global gene expression patterns in wheat. Keywords: time cource, stress response Overall design: Microarray hybridization was performed by a competitive two-color method including color-swap experiments. Chinese Spring wheat was grown for two weeks and treated with 150mM NaCl for 0, 1, 6 and 24 hours. RNA samples were extracted from roots and shoots.Each experiment was design for comparison in control and treated sample.

INSTRUMENT(S): wheat 22k

ORGANISM(S): Triticum aestivum  

SUBMITTER: Kanako Kawaura 

PROVIDER: GSE8060 | GEO | 2007-10-02

SECONDARY ACCESSION(S): PRJNA105397

REPOSITORIES: GEO

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