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E-MEXP-1344
Arabidopsis thaliana
6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis plants growing under diurnal conditions were transferred to cold of approximately one day duration, starting at different times of the day. All comparisons are of unreplicated pairs and are thus not designed to identify cold-responsive gens in isolation but are rather to supplement existing publicly available data. The overall aim was to use a diverse set of experiments to see which factors have the greatest influence on the identity of cold-responsive genes.
Publication Title
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
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.
Publication Title
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
In order to identify candidate target genes of the OBP1 (At3g50410) transcription factor we used dexamethasone inducible system (Lloyd et al, 1994). A single inducible over-expression line was compared to an empty vector control line 10h after DEX induction to identify candidate genes that were confirmed by quantitative RT-PCR.
Publication Title
The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana.
Sample Metadata Fields
Specimen part
View Samples