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The rcf1-1 mutation affects global gene expression in Arabidopsis thaliana with or without cold stress.

ABSTRACT: Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarrays to reveal the effect of rcf1-1 mutation on global gene expression with or without cold stress at 4°C. A set of genes differentially expressed in rcf1-1 with or without cold stress are identified.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE39090 | GEO | 2013/02/25

SECONDARY ACCESSION(S): PRJNA169923

REPOSITORIES: GEO

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The rcf1-1 mutation affects global gene expression in Arabidopsis thaliana with or without cold stress.

Project description:Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarrays to reveal the effect of rcf1-1 mutation on global gene expression with or without cold stress at 4M-BM-0C. A set of genes differentially expressed in rcf1-1 with or without cold stress are identified. Fourteen-day-old seedlings of Arabidopsis thaliana wild type (Columbia gl1 expressing CBF2::LUC transgene) and rcf1-1 mutant seedlings subjected to cold stress at 4M-BM-0C for 0, 12, and 24 h were used for total RNA extraction and hybridizations with Affymetrix ATH1 GeneChips. There are two biological replicate per genotype.

2013-02-25 | E-GEOD-39090 | biostudies-arrayexpress

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The rsa1-1 mutation affects global gene expression in Arabidopsis thaliana with or without salt stress

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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.

Project description: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 4M-BM-0C 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.

2013-02-25 | E-GEOD-41378 | biostudies-arrayexpress

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

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

Project description: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 normal growth conditions 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) under normal conditions were harvested for total RNA isolation. 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.

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Simmondsia chinensis leaf under cold stress, ITRAQ

Project description:Jojoba (Simmondsia chinensis) is a new semi- arid, oil- producing industrial crop that has attracted much attention in recent years. Low temperature is one of the major environmental stress that impairs plant growth and development. To better understand the molecular mechanisms of cold stress adaptation and acclimation of jojoba plants, a quantitative proteomic analysis using iTRAQ technology was conducted to detect the effects of cold stress on protein expression profiles in jojoba seedlings. Our work provided useful infomation for understanding the cold stress response and cold acclimation in jojoba.

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