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We used MethylCap-seq data obtained from artificially prepared fully unmethylated and fully methylated DNA samples for normalization of the data and assignment of DMRs.
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Levels of RNA polymerase II were used for normalization of the data.
A single copy gene, At5g47480, was used as an internal control for normalization of the data.
A tomato actin gene was used as an internal control for normalization of the data obtained.
The MAS5.0 algorithm of the GCOS program (Affymetrix, Santa Clara, CA) was used for normalization of the expression data.
The necessity for normalization of the raw data was demonstrated, without the method being very sensitive to the type of normalization.
For this reason, cons7 was selected for normalization of the expression data.
The Robust Multichip Average function was applied for normalization of the microarray data [ 74].
The housekeeping gene phosphofructokinase was used for normalization of the expression data.
β2‐Microglobulin was used as house-keeping gene for normalization of the mRNA expression data.
The GAPDH gene was used for normalization of the qSS-RT-PCR data.
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