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MeDIP-Microarray Analysis

KD Kostiantyn Dreval
VT Volodymyr Tryndyak
AC Aline de Conti
FB Frederick A. Beland
IP Igor P. Pogribny
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Methylated DNA immunoprecipitation was performed with MagMeDIP kits (Diagenode, Denville, NJ, United States) using 1 μg of genomic DNA isolated from full-fledged HCC (20 weeks) tissue samples and from liver tissue samples of corresponding age-matched control mice. The immunoprecipitated DNA and input DNA pellets were labeled with cyanine 5-dUTP and cyanine 3-dUTP, respectively, using Agilent SureTag DNA Labeling kits (Agilent Technologies, Santa Clara, CA, United States). The data acquisition and analysis was performed as described in Tryndyak et al. (2016). A list of differentially methylated CGIs was generated by calculation of Benjamini–Hochberg adjusted p-values (Benjamini and Hochberg, 1995) to control the FDR in multiple testing data, with an adjusted p-value cut-off 0.05, and a Z-score fold-change threshold of 1.5.

Copyright and License information:  ©2019 Dreval, Tryndyak, de Conti, Beland and Pogribny.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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