looking for normal cancer WGBS data

Question

[iiiiloveii19]

Hello,

I am working on a research with my professor on identifying hemimethylation on breast cancer and normal breast samples. We do have breast cancer samples, however we do not have normal breast samples to compare our result to the number of HM CG sites identified in normal breast.

Is there any normal breast WGBS data that is publicly available for research purpose??

I would greatly appreciate for any help I can get!

Thank you

Answer 1

[Mike]

If you search ENCODE for WGBS, Homo sapiens, and mammary gland there are 7 results (though they have some warnings, could just be a metadata issue):

https://www.encodeproject.org/search/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&organ_slims=mammary+gland&limit=all&assay_title=WGBS

You can also search GEO for 'wgbs' or 'whole genome bisulphite' plus 'breast' or 'mammary' and there are a few results (some might be duplicates as what's on ENCODE). GEO also has filters for assay type, species, etc. but I find they don't always work well. https://www.ncbi.nlm.nih.gov/geo/