Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.

ABSTRACT: Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under cold stress to identify transcripts which are mis-spliced/intron-retained in rcf1-1. Fourteen-day-old wild type and rcf1-1 seedlings grown on MS agar medium (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were subjected to cold stress at 4°C for 12 h. Total RNA was extracted with Trizol reagent (Invitrogen) and synthesized into double-stranded DNA that was hybridized to whole genome tiling arrays (Affymetrix Arabidopsis Tiling1.0R). All hybridizations were performed with 3 biological replicates.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Jianhua Zhu   Renyi Liu  Changhua Jiang  Chenglin Chai  Qingmei Guan  Yanyan Zhang  Jianmin Wu  Jianhua Zhu 

PROVIDER: E-GEOD-41378 | ArrayExpress | 2013-02-25

SECONDARY ACCESSION(S): GSE41378PRJNA176718

REPOSITORIES: GEO, ArrayExpress