Transcriptomics

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Development of a high-density oligo microarray of cassava, an important tropical crop


ABSTRACT: We developed a 60-mer oligonucleotide Agilent microarray representing about 20,000 cassava genes and applied it to expression profiling under drought stress. We demonstrated that our microarray is an useful tool for analyzing the cassava transcriptome and that it can be applied to various cassava species. After cutting of shoots from the cassava plants, the shoots were grown in a glass bottle containing MS medium supplemented with 2% sucrose and 0.3% gelrite for 4 weeks (16 hours light / 8 hours dark). The plantlets were subjected to drought treatment by removing the plantlets from the gelrite plate, placing on a plastic plate and keeping them for 1 hour under 40-80 μmol photons m-2 sec-1 at 30ºC in 50% of relative humidity. Then total RNA was prepared from the shoots and used for the microarray hybridization. Three replicative hybridization experiments were carried out using the independent biological samples.

SUBMITTER: Motoaki Seki   Manabu Ishitani  Morosawa Taeko  Akihiro Matsui  Kazuo Shinozaki  Atsushi Kurotani  Yoshinori Utsumi  Yoshimi Umemura  Takuhiro Yoshida  Maho Tanaka  Tetsuya Sakurai 

PROVIDER: E-GEOD-31749 | ArrayExpress | 2012-06-14

SECONDARY ACCESSION(S): GSE31749PRJNA145325

REPOSITORIES: GEO, ArrayExpress

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Publications

Transcriptome analysis using a high-density oligomicroarray under drought stress in various genotypes of cassava: an important tropical crop.

Utsumi Yoshinori Y   Tanaka Maho M   Morosawa Taeko T   Kurotani Atsushi A   Yoshida Takuhiro T   Mochida Keiichi K   Matsui Akihiro A   Umemura Yoshimi Y   Ishitani Manabu M   Shinozaki Kazuo K   Sakurai Tetsuya T   Seki Motoaki M  

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes 20120522 4


Cassava is an important crop that provides food security and income generation in many tropical countries and is known for its adaptability to various environmental conditions. Despite its global importance, the development of cassava microarray tools has not been well established. Here, we describe the development of a 60-mer oligonucleotide Agilent microarray representing ∼20,000 cassava genes and how it can be applied to expression profiling under drought stress using three cassava genotypes  ...[more]

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