PGS Documentation

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Illumina’s MethylationEPIC array interrogates the methylation status of over 850,000 cytosines in the human genome. Since the MethylationEPIC array is closely related to the Infinium HumanMethylation450 BeadChip, the steps presented in this document can be applied to either platform. The analysis laid out in the tutorial is based on detection of differentially methylated CpG sites and their subsequent filtering and annotation.

 

 

Due to annotation changes, the results presented here may slightly differ over the time.

 

Description of the Data Set

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 accession 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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