Transcriptomics,Multiomics

Dataset Information

181

Transcription profiling of Arabdiposis plants before and after cold treatment using spike-in controls to allow measurement of absolute mRNA expression at the global level


ABSTRACT: To address the neglected possibility for global mRNA changes in microarray experiments we developed a simple method to generate external controls for Affymetrix microarrays to allow these platforms to measure absolute mRNA expression at the global level. We used publicly available data to select probesets that never detect endogenous transcripts, and used PCR and IVT to generate synthetic mRNAs corresponding to them. After quality control and testing, these control transcripts were spiked into total RNA samples from plants before and after 24 h of cold treatment. Due to changes in the proportion of mRNA, these data reveal intensity-dependent bias in expression estimates based on standard all-gene normalizations. When not accounted for, this leads to false classification of the differential expression for thousands of genes.

REANALYSIS of: E-MEXP-1345

ORGANISM(S): Arabidopsis thaliana  

PROVIDER: E-MEXP-1345 | ExpressionAtlas | 2014-08-16

REPOSITORIES: ExpressionAtlas

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Publications

Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.

Bieniawska Zuzanna Z   Espinoza Carmen C   Schlereth Armin A   Sulpice Ronan R   Hincha Dirk K DK   Hannah Matthew A MA  

Plant physiology 20080328 1


In plants, low temperature causes massive transcriptional changes, many of which are presumed to be involved in the process of cold acclimation. Given the diversity of developmental and environmental factors between experiments, it is surprising that their influence on the identification of cold-responsive genes is largely unknown. A systematic investigation of genes responding to 1 d of cold treatment revealed that diurnal- and circadian-regulated genes are responsible for the majority of the s  ...[more]

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