Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing.
Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing.
复制标题
使用高通量靶向重复元件亚硫酸氢盐测序对 ES、体细胞和癌细胞中的逆转录转座子进行位点特异性 DNA 甲基化分析。
DOI：
10.1016/j.gdata.2014.11.013
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Kim,Joomyeong
中科院分区：
文献类型：
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作者：
Bakshi,Arundhati;Ekram,MuhammadB;Kim,Joomyeong
DNA甲基化是一个主要的表观遗传标记，与哺乳动物基因组中反转录转座子的多个方面相关。为了在个体位点的基础上研究大量逆转录转座子的DNA甲基化，我们开发了一种新的方案，称为高通量靶向重复元件亚硫酸酯测序（HT-TREBS） （Ekram和Kim， 2014[1]）。我们使用该技术表征了胚胎干细胞、体细胞和神经2a细胞中小鼠IAP LTR（胞内A粒子长末端重复）逆转录转座子家族4799个成员的基因座特异性DNA甲基化模式（Bakshi和Kim， 2014[2]）。在这里，我们详细描述了用于这些研究的样品制备和生物信息学分析。体细胞数据可以在GEO登录号GSE49222下访问。ES和Neuro2A数据保存在GEO登录号GSE60007下。
DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a new protocol termed High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS) (Ekram and Kim, 2014 [1]). We have used this technique to characterize the locus-specific patterns of DNA methylation of 4799 members of the mouse IAP LTR (Intracisternal A Particle Long Terminal Repeat) retrotransposon family in embryonic stem, somatic and Neuro2A cells (Bakshi and Kim, 2014 [2]). Here we describe in detail the sample preparation and bioinformatics analyses used for these studies. The somatic cell data may be accessed under GEO accession number GSE49222. The ES and Neuro2A data are deposited under GEO accession number GSE60007.