Illumina Inifinium HumanMethylation450 array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment

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 (Darmkrebs: Chancen der Verhuetung durch Screening, http://dachs.dkfz.org/dachs/), 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).

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.

References:

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.

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.

本数据集包含38对配对样本的原始甲基化（M）与非甲基化（U）信号强度，每一例样本均配有癌组织（非转移性结直肠癌）与健康组织（正常黏膜）。本数据来源于正在进行的基于人群的病例对照研究DACHS（全称：Darmkrebs: Chancen der Verhütung durch Screening，http://dachs.dkfz.org/dachs/），相关细节已在Brenner等于2011年的研究中详尽阐释。数据采集、患者招募流程，以及采用Infinium HumanMethylation450 BeadChip芯片（Illumina）开展的DNA分离与甲基化图谱分析流程，均与Gündert等于2017年的研究描述一致。

在本实验框架下，全部38例样本均通过配对的亚硫酸氢盐（bisulfite, BS）与氧化亚硫酸氢盐（oxidative bisulfite, oxBS）处理流程完成制备。采用此类配对处理的原因在于：常规用于获取M与U信号强度的BS处理仅能区分甲基化与非甲基化胞嘧啶碱基，无法分辨5-甲基胞嘧啶（5mC）与5-羟甲基胞嘧啶（5hmC）。为测定目标核苷酸位点的5hmC水平（这是本研究开展5hmC量化分析的必要前提），我们应用了oxBS处理流程。所采用的处理方式（BS或oxBS）以及对应的信号强度类型（M或U），均可从对应文件名中获取。每个文件包含77列：第一列为对应CpG位点的标识，剩余76列按交替顺序依次给出健康组织与癌组织的信号强度。

参考文献：
Brenner H, Chang-Claude J, Seiler CM 等. 结肠镜检查后结直肠癌的保护作用：一项基于人群的病例对照研究. 《内科学年鉴》（Ann Intern Med）2011; 154: 22-30.
Gündert M, Edelmann D, Benner A 等. 全基因组DNA甲基化分析揭示非转移性结直肠癌的预后分类器（ProMCol分类器）. 《肠道》（Gut）2017; 1-10.