A list of PCR2-ageindex CpGs for Illumina 450k and EPIC arrays

[karoliskoncevicius]

Hello and congratulations with the publication.

Not sure if this is a place to ask - but I was wondering, is there a list of Illumina methylation microarray CpGs used by your PCR2 aging index? I went through the paper and supplements, but didn't find it.

[AaronBlare]

I faced the same problem.
The PRC2-AgeIndex in the paper is calculated for 450k methylation (among others), but there is no list of CpG sites in the text, in the supplementary, or in this repository.
Files with the code that should build Figures 3 and 4 refer to files with methylation data of different GSEs (from which a list of CpGs could be extracted), but they are missing in the repository.

[moqri]

@dsimps1993 , can you please add the lists to the repository? (we are all good with the IP now)

[dsimps1993]

Apologies for the wait!

Top 1000 low methylated CpGs (LMCs) has been added to PRC2-AgeIndex_Manuscript_Figures/results as Top1000_ArrayPRC2bind_LMCs.csv
Full list of LMCs sorted by PRC2 binding (Pr) has also been added as ArrayPRC2bind_LMCs.csv

Top 1000 low methylated regions (LMRs) for various tissues (Top1000_PRC-LMRs_WGBS.xlsx) as also been added to the same folder.

Cheers,

Dan