Reduced-Representation Bisulphite Sequencing Data In Encode

Question

[pengcui1989]

Dear all!

I am very interested in the DNA methylation data from ENCODE. However, I have a question about the data. I know that in ENCODE, many experiments are conducted on the same cell line according to the same cell culture protocol, for example, the chip-seq data or the RNA-seq data. And they all write 'Cells were grown according to the approved ENCODE cell culture protocols' in their methods. So we can analysis these datasets together.

I want to know that if RRBS of all cell lines also follow the same cell culture protocols or not. So we can make a comprehensive analysis with other datasets( RNA-seq or others) in the same cell line?

[Neilfws]

RRBS = reduced-representation bisulphite sequencing. Always best to define your abbreviations on first use, not everyone instantly knows what you are talking about.

Answer 1

[Neilfws]

I think you can use the ENCODE Experiment Matrix to answer this question.

[pengcui1989]

I'm sorry. I don't know. ??

Answer 2

[Mary]

Part of the goal was as much standardization as possible so comparisons could be made. But you can see the protocols attached to each cell line here: http://www.encodeproject.org/ENCODE/cellTypes.html and I would look closely at the documents there.

[pengcui1989]

I'm sorry that I havn't explained my question clearly. I want to know that whether the RNA-seq, Chip-seq, RRBS experiments in the same cell line are conducted in the same condition. So we can analysis these datasets together. For example. in hESC cell line, if it is cultured in 30 centigrade, they make the RNA-seq. And in 15 centigrade, they make the RRBS. So we can't analysis them together, because they have different cuture conditions.