Dataset Information

Comparison of WT and YODA

ABSTRACT: Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination (~150 micromoles per square meter per second) at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synthesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions. Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500. Keywords = yoda Keywords = yda Keywords = kinase Keywords = MAPKKK Keywords: parallel sample

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE919 | GEO | 2003/12/30

SECONDARY ACCESSION(S): PRJNA87937

REPOSITORIES: GEO

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Project 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 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

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Comparison of WT and YODA

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