Individual CpG site methylation data


I believe that in the past the Broad Institute CCLE website included Illumina 450k methylation data for most cell lines. However, these no longer seem to be available, as I can only find links to RRBS methylation data. Are these individual CpG site-level methylation data still available for download?

Thank you.

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I’m not familiar with the existence of Illumina 450k data for CCLE lines.

Skimming through “Next-generation characterization of the Cancer Cell Line Encyclopedia” I see that it primarily talks about the RRBS data that I’m familar with:

Genome-wide DNA promoter methylation
To address the role of DNA methylation on mRNA expression and
consequent changes in gene dependence, RRBS analysis was used to
assess promoter methylation. Previously microarray-based methylation data for a subset of the CCLE cell lines was reported (n = 655
overlapping cell lines)

The “microarray-based methylation data” looks like it’s what you’re looking for. That references a paper “A Landscape of Pharmacogenomic Interactions in Cancer” which reports to have Illumina 450k for a set of lines. From the text in the CCLE paper, it sounds like 655 lines were in the CCLE collection at that time.

That paper points to GEO Accession viewer for accessing the methylation data.

This data definitely does sound potentially useful to have on the portal, but I don’t believe it was available as a download file in the previous CCLE portal because we were fairly careful about making sure we kept all files when we changed the portal.

Is it possible that you couldn’t download it in bulk, but you could view it interactively in plots? That might explain how we didn’t notice it was missing in the new version.

Regardless, it appears the dataset is available for download and now that I know of this data’s existence, I suspect there may be value in adding this to the interactive plots in the portal. (But that will take some time)