Roadmap Epigenomics Project Sample Amalgamation of Same Tissue?

Question

[Shicheng Guo]

Hi All,

I download the 5mC methylation (WGBS) data from Roadmap Epigenomics Project. However, I found only 37 column were existed in the FractionMethylation (fm) files?

http://egg2.wustl.edu/roadmap/data/byDataType/dnamethylation/WGBS/

But I know there are several biological replications in Epigenome Roadmap Project. Why only one tissue was existed in the finally file? such as STL002EG and STL003EG.

STL002EG-01 Esophagus STL003EG-01 Esophagus

Thanks.

Answer 1

[Shicheng Guo]

Okay. I have receive the reply from Dr. Misha Bilenky. I still keep the record here so that It would be helpful for others.

That is correct - for several tissues/ cell types there were more than one replicates. The consortium decided to combine those to increase coverage of CpGs. As result there is just one data column per tissue.

Best,

Misha Bilenky

Answer 2

[zhisheng.qian]

Does the -1 in WGBS FractionMethylation (fm) files means missing value?