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Data were calculated with LinReg PCR 7.0 and Q-Gene software and then expressed as mean normalized expression (MNE) units after GAPDH normalization.
Amplification plots have been analyzed using Opticon Monitor software version 2.02 (MJ Research, Waltham, MA, USA) and data calculated with Q-Gene software (www.BioTechniques.com) and expressed as mean normalized expression (MNE).
Data analyses were performed using Q-gene qRT-PCR analysis software (Gene Quantification (http://www.gene-quantification.info/) [44] and results were expressed as Mean Normalized Expression (MNE) relative to the reference gene.
qRT-PCR data analyses used the Relative Expression Software Tool (REST) and were expressed as Mean Normalized Expression (MNE) relative to the reference gene [ 40].
For any sample the expression level was analyzed using Q-Gene® software, which expresses data as mean normalized expression.
Data were expressed as medians of mean normalized expression with standard deviation (SD).
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Mean-normalized expression values were transformed into log values.
The candidate genes were grouped according to predicted function in specific modified nucleosides and mean-normalized expression values from the AtGenExpress database were transformed into log values for heat map construction using MeV (MultiExperiment Viewer) software.
The mRNA expression of SOCS2, SOCS3, CIS, IGF-1 and GHR was defined as the mean normalized gene expression (MNE) difference in target gene expression relative to the 'housekeeping gene' 18S rRNA using the following equation [ 18]: MNE = [(Eref CTref,mean]/[(Etarget CTtarget,mean].
Bars represent mean normalized surface expression.
This showed a mean normalized gene expression ratio of +32.0 for Tnf mRNA (P<0.05: randomization test).
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