Genome-wide DNA Methylation Analysis

DNA was extracted from 1×10⁶ cells (QIAGEN DNeasy Blood and Tissue Kit), quantified (Qubit dsDNA BR Assay Kits, Life Technologies), quality controlled (DNA1000 Kit and BioAnalyzer 2100, Agilent), and bisulfite converted (EZ DNA Methylation Kit, Zymo Research) according to each manufacturer's protocol. Bisulfite-converted DNA was hybridized to Infinium-450 BeadChips (Illumina) and scanned with an iScan (Illumina). Quality control was performed in GenomeStudio. HumanMethylation450 data were normalized using SWAN (Maksimovic et al., 2012 (link)) and differential methylation was identified using Limma (Smyth, 2004 (link)). Hierarchical clustering was performed using Cluster, with Euclidian distance and complete linkage. Functional enrichments were executed in GREAT (McLean et al., 2010 (link)) using default settings. DNA methylation data have been deposited in Gene Expression Omnibus under accession number GSE63592.

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Zdravkovic T., Nazor K.L., Larocque N., Gormley M., Donne M., Hunkapillar N., Giritharan G., Bernstein H.S., Wei G., Hebrok M., Zeng X., Genbacev O., Mattis A., McMaster M.T., Krtolica A., Valbuena D., Simón C., Laurent L.C., Loring J.F, & Fisher S.J. (2015). Human stem cells from single blastomeres reveal pathways of embryonic or trophoblast fate specification. Development (Cambridge, England), 142(23), 4010-4025.

Publication 2015

DNeasy Blood and Tissue Kit Qubit dsDNA BR Assay Kits DNA1000 Kit BioAnalyzer 2100 EZ DNA Methylation Kit

Assay Bisulfite Blood Cells Dna methylation Dsdna Gene expression Iscan Methylation Tissue

Corresponding Organization :

Other organizations : University of California, San Francisco, Broad Center, Reproductive Science Center, Scripps Research Institute, Buck Institute for Research on Aging, Valencian Infertility Institute, Universitat de València, University of California, San Diego

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

DNA methylation levels

control variables

None explicitly mentioned

controls

Positive control: None mentioned
Negative control: None mentioned

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