Affymetrix GeneChip Arabidopsis Genome [AG]

Gating of the rapid shade avoidance response by the circadian clock in plants

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This experiment was a time course performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants. In this way genes involved in the shade avoidance response might be identified. This experiment was designed for gene identification only and containes no replicates,genes identified were verified by quantitative PCR for publication.

Transcription profiling time course experiment performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants

This experiment was a time course performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants. In this way genes involved in the shade avoidance response might be identified. This experiment was designed for gene identification only and containes no replicates,genes identified were verified by quantitative PCR for publication.


Affymetrix:Protocol:Hybridization-EukGE-WS2v4[]

Title: Affymetrix EukGE-WS2v4 Hybridization. Description:

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-AFFY-7

P-MEXP-1715

Samples consisted of predominantly leaf tissue and RNA was extracted using QIAGEN RNeasy midi kits in accordance with the manufacturer’s instructions. Following extraction the RNA was subjected to extraction with acid phenol followed by extraction with chloroform: isoamyl alcohol 24:1 and ethanol precipitation to a final concentration > 3 mg/ml. Sample tubes were marked with time point and either W for high R:FR ratio control samples and FR for low R:FR ratio-treated samples. Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled UTP and CTP. The biotin labelled cRNA is fragmented and hybridised to the Arabidopsis array and stained with phycoerythrin-streptavidin and scanned to generate the raw image dat file.

P-MEXP-1716

Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled UTP and CTP. The biotin labelled cRNA is fragmented and hybridised to the Arabidopsis array and stained with phycoerythrin-streptavidin and scanned to generate the raw image dat file.

P-MEXP-1774

Arabidopsis plants grown to 11 leaves in light dark cycles. An amalgam of 6 individuals was harvested after 1 h of high red:far red ratio light on day 1 for total RNA extraction. Samples consisted of predominantly leaf tissue and RNA was extracted using QIAGEN RNeasy midi kits in accordance with the manufacturer’s instructions. Following extraction the RNA was subjected to extraction with acid phenol followed by extraction with chloroform: isoamyl alcohol 24:1 and ethanol precipitation to a final concentration > 3 mg/ml. Sample tubes were marked with time point and either W for high R:FR ratio control samples and FR for low R:FR ratio-treated samples. Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled 

P-MEXP-1779

Arabidopsis plants grown to 11 leaves in light dark cycles. An amalgam of 6 individuals was harvested after 2 h of high red:far red ratio light on day 1 for total RNA extraction. Samples consisted of predominantly leaf tissue and RNA was extracted using QIAGEN RNeasy midi kits in accordance with the manufacturer’s instructions. Following extraction the RNA was subjected to extraction with acid phenol followed by extraction with chloroform: isoamyl alcohol 24:1 and ethanol precipitation to a final concentration > 3 mg/ml. Sample tubes were marked with time point and either W for high R:FR ratio control samples and FR for low R:FR ratio-treated samples. Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled  

P-MEXP-1780

Arabidopsis plants grown to 11 leaves in light dark cycles. An amalgam of 6 individuals was harvested after 1 h of high red:far red ratio light on day 1 plus 1 h low red :far red light for total RNA extraction. Samples consisted of predominantly leaf tissue and RNA was extracted using QIAGEN RNeasy midi kits in accordance with the manufacturer’s instructions. Following extraction the RNA was subjected to extraction with acid phenol followed by extraction with chloroform: isoamyl alcohol 24:1 and ethanol precipitation to a final concentration > 3 mg/ml. Sample tubes were marked with time point and either W for high R:FR ratio control samples and FR for low R:FR ratio-treated samples. Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled  

P-MEXP-1781

Arabidopsis plants grown to 11 leaves in light dark cycles. An amalgam of 6 individuals was harvested after 9 h of high red:far red ratio light on day 1 for total RNA extraction. Samples consisted of predominantly leaf tissue and RNA was extracted using QIAGEN RNeasy midi kits in accordance with the manufacturer’s instructions. Following extraction the RNA was subjected to extraction with acid phenol followed by extraction with chloroform: isoamyl alcohol 24:1 and ethanol precipitation to a final concentration > 3 mg/ml. Sample tubes were marked with time point and either W for high R:FR ratio control samples and FR for low R:FR ratio-treated samples. Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled  

P-MEXP-1782

Arabidopsis plants grown to 11 leaves in light dark cycles. An amalgam of 6 individuals was harvested after 8 h of high red:far red ratio light followed by 1 h low red:far red ratio light on day 1 for total RNA extraction. Samples consisted of predominantly leaf tissue and RNA was extracted using QIAGEN RNeasy midi kits in accordance with the manufacturer’s instructions. Following extraction the RNA was subjected to extraction with acid phenol followed by extraction with chloroform: isoamyl alcohol 24:1 and ethanol precipitation to a final concentration > 3 mg/ml. Sample tubes were marked with time point and either W for high R:FR ratio control samples and FR for low R:FR ratio-treated samples. Labelling for hybridisation was completed using Enzo Life Sciences BioArray™ HighYield™ RNA Transcript Labeling kit. Biotin-labeled RNA is produced by T7 RNA polymerase-catalyzed in vitro transcription in the presence of biotin-labeled  

P-MEXP-1785

In vitro transcription by using double-stranded cDNA as a template in the presence of biotinylated UTP and CTP, using an ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA, and ENZO Diagnostics, Farmingdale, NY) according to the manufacturer’s instructions. 

Transcription profiling time course experiment performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants

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