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The data set accompanying this document consists of eight human samples processed by Illumina MethylationEPIC  BeadChip arrays. The data set is taken from a study of DNA methylation in human pluripotent stem cells (hPCS) (Lee et al. Cell Rep 2017). The data set includes naive hPSCs, which can only differentiate into neural fate cells in vitro; primed hPSCs, which have multi-germ layer potential in vitro, but must be derived from native hPSCs over long-term serial passage under primed culture conditions; naive hPSCs treated with small hairpin RNAs (shRNAs) targeting OCT4; and native hPSCs treated with shRNAs targeting NANOG. The authors hypothesized that the higher expression of the core pluripotent genes OCT4 and NANOG in naive vs. primed hPSCs is responsible for the reduced differentiation capacity of naive hPSCs by enhancing self-renewal at the expense of differentiation capacity. 

The data files can be downloaded from Gene Expression Omnibus using the following accession number: number GSE95531. To follow this tutorial, download the 16 .idat files associated with GSE95531 (note that two .idat files are generated for each array) and unzip them on your local computer. 

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