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2 results for “oxidative bisulfite treatment”
Illumina Inifinium HumanMethylation450 array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment
<p>The current data sets represent the raw methylated (M) and unmethylated (U) intensities on 38 paired samples, with cancer (non-metastatic colorectal cancer) and healthy (normal mucosa) tissue available for each single sample. The data were obtained in the context of the ongoing population-based case-control study DACHS (<em>Darmkrebs: Chancen der Verhuetung durch Screening</em>, <a href="http://dachs.dkfz.org/dachs/">http://dachs.dkfz.org/dachs/</a>), extensively described in Brenner et al. (2011). Data collecting and patient recruitment procedures as well as the processes of DNA isolation and methylation profiling using the Infinium HumanMethylation450 BeadChip array (Illumina) are similar to those described in Gündert et al. (2017).</p> <p>In the context of our experiment, all 38 samples were handled by means of paired bisulfite (BS) and oxidative bisulfite (oxBS) procedures. The reason for such paired treatment is the fact that the BS procedure, commonly used for derivation of the M and U intensities, can only differentiate between methylated and unmethylated cytosine bases, and cannot discriminate between 5mC and 5hmC. In order to determine the level of 5hmC at a considered nucleotide position that is indispensable for our analyses of the 5hmC measures, the oxBS procedure was applied. The name of the applied procedure (BS or oxBS) as well as the name of the corresponding intensities (M or U) can be read off from the name of the corresponding file. Each file contains 77 columns. The first column provides the designation of the corresponding CpG, the remaining 76 columns provide the corresponding intensities on healthy and cancer tissue, in alternating order.</p> <p>References:</p> <p>Brenner H, Chang-Claude J, Seiler CM et al. Protection from colorectal cancer after colonoscopy: a population-based, case-control study. Ann Intern Med 2011; 154: 22-30.</p> <p>Gündert M, Edelmann D, Benner A, et al. Genome-wide DNA methylation analysis reveals a prognostic classifier for non-metastatic colorectal cancer (ProMCol classifier). Gut 2017; 1-10.</p>
High grade glioma methylation analysis using bisulfite and oxidative bisulfite-treatment
GEO Series GSE104723. Homo sapiens. 42 samples. Type: Methylation profiling by array.
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