E-GEOD-1111 - Transcription profiling by array of Arabidopsis after treatment with indole-3-acetic acid
Released on 27 October 2007, last updated on 1 March 2012
Arabidopsis seedlings (Col-0) were grown in suspension in half-strength MS medium with agitation at ~100 rpm at ~22 C under ~50 microeinsteins m-2s-1 cool white fluorescent continuous illumination as described by (Xiao et al., Plant Physiol. 2002 Dec;130(4):2118-28). Seedlings were treated at 10-12 days by addition of freshly made IAA; (0.1 or 1.0uM) to each flask, and harvested after a 1 or 3 hour incubation. Controls were not treated and harvested at 0hr. All tissue harvested. Total RNA was extracted using TRIzol (Invitrogen) as described by the manufacturer and then filtered using QIAGEN RNeasy columns. cDNA was synthesized from total RNA using a Superscript double-stranded cDNA; synthesis kit (Invitrogen) and a T7-dT24 primer. cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling kit (Affymetrix p/n 900182) and fragmented by Mg2+ hydrolysis. 15ug per array was hybridized overnight at 45 C. Arrays were then; washed and scanned using the GeneChip FS400 fluidics station and Agilent GeneArray scanner. Images were analyzed using Affymetrix Microarray Suite 5.0, scaling to a target average; intensity of 500. Spiking controls were added to the total RNA before cDNA synthesis and additional spiking samples were added to the resulting cDNA prior to cRNA synthesis. Probe samples were recovered for use in replicate hybridizations, 2 per array for a total of 4 hybridizations. The purpose of this was the statistical comparison of the two different versions of Affymetrix Arabidopsis probe arrays, AG and ATH1, as part of the process of characterization of the newer array, ATH1. A complete dose response assay using ATH1 and the data represented below may be found in series file GSE1110. In comparison table below:; SIGNAL_LOG_RATIO = Mean of log to base two of the experimental divided by control signal ratios across all probe pairs in a set. CHANGE = Qualitative measurement indicating whether the probe set signal is increased (I), marginally increased (MI), not changed (NC), marginally decreased (MD), or decreased (D) as compared to a control hybridization across all probe pairs, based on a p-value calculation. change_p-value = Measures the probability that all probe pairs in the set indicate a change, with 0 indicating strong likelyhood for increase, 0.5 indicating little probability for difference, and 1 indicating strong probability for decrease.
transcription profiling by array, array platform variation, co-expression, dose response, time series
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Julia C Redman,Brian J Haas,Gene Tanimoto,Christopher D Town. , Europe PMC 15086809