Methylation coordinates for hg19

Question

[Parham]

Hi,

Are there any resources to grab the coordinates of the genome with known methylation sites and coordinates, be it tissue specific or more general methylation landscape? If there are any databases I can extract this information from I would be very happy to know.

Answer 1

[lily]

ENCODE provides useful methylation data for the human genome. They also provide a lot of tissue specific methylation data.

https://www.encodeproject.org/matrix/?type=Experiment&status=released&assay_slims=DNA+methylation&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&award.project=ENCODE&assembly=hg19

As you are searching for specific CpG sites, you should filter for arrays with appropriate resolution such as RRBS.

[Parham]

Thanks for introducing Encode. It seems that they have bunch of methylation data for different cell lines or tissues in human. However they seem to be a bit aged now being from early 2010s and I wonder why most recent research data with more recent methods and sequencing resolution is not uploaded. I also would like to see something that had methylation data for specific cancers but that seems to be hard to find in databases. Do you have any recommendation for that as well?

[lily]

If you are looking for more recently published data you should also consider methylation data in hg38 annotation, there seem to be newer ones available at ENCODE.