Methylation array

Methylation profiling by array is used to probe the methylation pattern of DNA, which is a suppressor of gene activity. Methylation is used in HipSci’s assessment of variability in the pluripotent phenotype, and it’s dependence on genetic and techncial factors.

HipSci assays iPS cell lines that are selected for banking after they have passed QC, typically one cell line per donor. The assay uses the Illumina HumanMethylation450 BeadChip v1.0

Getting the data

Complete lists of methylation array data can be found under the files tab of the cell lines and data browser or in the dataset indexes on the FTP site.

  • Signal intensity data – Distributed in Illumina idat file format. This binary file can be read by Illumina software. There are two single-sample idat files for each cell line, corresponding to the red and green channels of the BeadChip.
  • Text files with probe intensities – Tab-delimited text files with probe intensities for each probe. We distribute one single-sample text file for each cell line.

For managed access cell lines, methylation array data files are archived in the EGA. The data browser contains links to the relevant EGA dataset page, from where researchers can request access to the data.

For open access cell lines, methylation array data files are archived in ArrayExpress. Data are openly available to anybody, and the data browser contains direct links to the files on the ArrayExpression files download page.