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Browse AraPLEX Experiment Data

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Indole acetic acid treatment-dose response and time course
Redman JC, Haas BJ, Tanimoto G, Town CD, The Institute for Genomic Research (jredman@tigr.org)
Experiment design (24 hybridizations)
compound
•IAA0.1um •IAA1um
time
•0hai •1hai •3hai

This is the part of ATH1 data from GEO experiment: Comparison of AG and ATH1 using IAA http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1111 ...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Indole acetic acid treatment-dose response and time course
Accession No: AT17
Microarray: ATH1-121501
Visibility: public
Experiment Type:
Experiment Factor(s):
compound
•IAA0.1um  •IAA1um
time
•0hai  •1hai  •3hai
Quality Control: biological replicates
Treatment summary:
 compound  time  # replicates
 IAA0.1um  0hai  4
 IAA0.1um  1hai  4
 IAA0.1um  3hai  4
 IAA1um  0hai  4
 IAA1um  1hai  4
 IAA1um  3hai  4
Total hybridizations: 24
Description: This is the part of ATH1 data from GEO experiment:
Comparison of AG and ATH1 using IAA
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1111

Series GSE1111 Query DataSets for GSE1111
Status Public on Mar 9 2004

Title Comparison of AG and ATH1 using IAA

Type parallel sample

Description 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.

Keyword IAA, whole plant, indole-3-acetic acid, Arabidopsis
Author Redman JC, Haas BJ, Tanimoto G, Town CD
Submission date Mar 5 2004

Submitter name Redman, Julia C
Submitter email jredman@tigr.org

Submitter institute The Institute for Genomic Research

Submitter laboratory Christopher Town

Submitter department Plant Genomics

Submitter address 9712 Medical Center Dr

Submitter city Rockville, MD 20850 USA
Submitter phone 301-795-7000

Submitter web link www.tigr.org

Sample id GSM18228, GSM18229, GSM18290, GSM18291, GSM18294, GSM18295, GSM18325, GSM18326, GSM18327, GSM18328, GSM18329, GSM18330
Publication: none
Created: 2004-11-03 16:45:37
Last Update: 2008-08-05 10:59:47
Submitter: Lishuang Shen
Name: Redman JC, Haas BJ, Tanimoto G, Town CD
Institution: The Institute for Genomic Research
Head of Laboratory: Christopher Town
email(s):
Homepage:

 
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