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Series GSE1110 Query DataSets for GSE1110
Status Public on Mar 09, 2004
Title Arabidopsis thaliana gene expression in response to IAA challange
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary 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 ATH1 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.

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.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Keywords = Arabidopsis
Keywords: dose response
Contributor(s) Redman JC, Haas BJ, Tanimoto G, Town CD
Citation(s) 15086809
Submission date Mar 05, 2004
Last update date Jun 12, 2017
Contact name Julia C Redman
Phone 301-795-7000
Organization name The Institute for Genomic Research
Department Plant Genomics
Lab Christopher Town
Street address 9712 Medical Center Dr
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (22)
GSM18228 Control_1.1 (a)
GSM18229 Control_1.2 (a)
GSM18230 Control_2.1
BioProject PRJNA87215

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