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Indole acetic acid treatment-dose response and time course | |||||||||||
| Experiment Name: | Indole acetic acid treatment-dose response and time course | ||||||||||
| Accession No. & GeneChip: | AT17, ATH1-121501 | ||||||||||
| Submitter: | Experimenter: Redman JC, Haas BJ, Tanimoto G, Town CD, submitted by Lishuang Shen | ||||||||||
| Experiment Type: | compound treatment time course | ||||||||||
| Experiment Factor: | compound time | ||||||||||
| Number of Replicates: | 4 | ||||||||||
| Quality Control Steps: | biological replicates | ||||||||||
| Quality Control Description: | None | ||||||||||
| Publication_id: | None | ||||||||||
| Last Update Time: | 2004-11-03 16:45:37 | ||||||||||
| Expression Data Access & Analysis: | Please select one action: 1. Batch download all data files at Download Center . 2. Browse Hybridizations and boxplots from experiment. 3. Visualization of hybridizations or treatment means with scatterplots and MvA plots. 4. Browse Samples from experiment. 5. Create Gene List by filter probe sets for differentially-expressed genes. 6. Pattern Recognition on filtered gene list. | ||||||||||
| 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 | ||||||||||
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