Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine

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The aim of the experiment is to determine sugar and ABA responsive gene expression in Arabidopsis.

growth condition

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Transcription profiling by array of Arabidopsis after treatment with glucose, mannose and abcissic acid

Transcription profiling of Arabidopsis treated with sugars (glucose, mannose) and abcissic acid

The aim of the experiment is to determine sugar and ABA responsive gene expression in Arabidopsis.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v4

Title: Fluidics Station Protocol. Description:

Affymetrix:Protocol:Hybridization-FlexGE-WS2v4

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-10341

Arabidopsis thaliana seedlings (ecotype Columbia-0) were grown in liquid culture for 7 days on MS medium containing 0.5% glucose in constant light. After 7days growth, the medium was replaced with glucose-free medium for 24 hrs.

P-MEXP-10342

Seedlings were treated with 3% glucose, 3% mannitol, 3% glucose + 10ƒÝM ABA or 3% mannitol + 10ƒÝM ABA, and sampled at 0, 2, 4 or 6 hours after treatment. Three independent sets of cultures grown in 3% glucose and 3% mannitol were sampled for RNA isolation.

P-MEXP-10346

Total RNA was extracted from the treated Arabidopsis seedlings using an RNeasy Plant Mini Kit (Qiagen, West Sussex, UK) according to the kit manual. 

P-MEXP-8187

Starting total RNA quality was assessed by running 1ul of each RNA sample on Agilent RNA6000nano LabChips (Agilent Technology 2100 Bioanalyzer Version A.01.20 SI211). Total RNA quantity was assessed by running 1ul of each RNA sample on a NanoDrop ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies). First strand cDNA synthesis was performed according to the Affymetrix Manual II, using 5ug of total RNA. Second strand cDNA synthesis was performed with minor modifications to the Affymetrix Manual II. Brieflly, cDNA termini were not blunt ended and the reaction was not terminated using EDTA. Instead Double-stranded cDNA products were immediately purified following the “Phase Lock Gel Cleanup of Double-Stranded cDNA” protocol (Affymetrix Manual II). cDNA was resuspended in 22ul of RNAse free water. cRNA preparation was performed with minor modifications to the Affymetrix Manual II.  Briefly, 11ul of cDNA was used as a template to produce biotinylated cRNA using half the recommended volumes of the ENZO BioArray High Yield RNA Transcript Labeling Kit. Labelled cRNAs were purified following the “Qiagen RNeasy Cleanup and Quantification of Biotin-Labeled cRNA” protocol (Affymetrix Manual II). cRNA quality was assessed by on Agilent RNA6000nano LabChips (Agilent Technology 2100 Bioanalyzer Version A.01.20 SI211). cRNA quantity was assessed by running 1ul of each cRNA sample on a NanoDrop ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies).

Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine.

Transcription profiling by array of Arabidopsis after treatment with glucose, mannose and abcissic acid

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