Unknown,Transcriptomics,Genomics,Proteomics

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Global gene expression levels in wild-type (Col-0), med18 and med25 mutant lines of Arabidopsis thaliana

ABSTRACT: Plants were grown in a mix (2:1) of soil and vermiculite in individual pots and cultivated in a growth chamber with 60-70% relative humidity and a day/night cycle (16hr-23°C/8h-20°C) at around 110 mol.m-2.s-1. For the microarray and metabolomic experiments, leaves of med18, med25, and WT were collected at the bolting time of WT. The experiments were repeated at least 3 times.Leaves of plants (mutants and WT) grown in LD conditions were collected, frozen and stored at –80°C until extraction. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen Nordic, Sollentuna, Sweden). For each sample the DNase treatment was performed during the extraction according to the Qiagen protocol with RNase-free DNase I (Qiagen) to eliminate genomic DNA contamination. ATH1 Affymetrix GeneChip microarrays were performed using 10 μg of total RNA per sample as described in the Affymetrix GeneChip technical analysis manual (Affymetrix UK Ltd, High Wycomb, UK). RNA integrity was checked by an Agilent Bioanalyzer. Microarray experiments were performed in the Affymetrix core lab of Nottingham Arabidopsis Stock Centre, Loughborough, UK. Normalization of raw intensities across all probe sets was performed in R language using Robust Multi-array Average (RMA) algorithms and using Bioconductor software (http://www.bioconductor.org). Three replicates of independently grown material were used.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Stefan Björklund

PROVIDER: E-MTAB-5748 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global gene expression levels in wild-type (Col-0), med18 and med25 mutant lines of Arabidopsis thaliana

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