Question: Reduced-Representation Bisulphite Sequencing Data In Encode
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gravatar for pengcui1989
6.4 years ago by
pengcui198930
Chiina
pengcui198930 wrote:

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?

encode sequencing • 1.9k views
ADD COMMENTlink modified 6.4 years ago by Mary11k • written 6.4 years ago by pengcui198930

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

ADD REPLYlink written 6.4 years ago by Neilfws48k
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gravatar for Neilfws
6.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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

ADD COMMENTlink written 6.4 years ago by Neilfws48k

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

ADD REPLYlink written 6.4 years ago by pengcui198930
0
gravatar for Mary
6.4 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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.

ADD COMMENTlink written 6.4 years ago by Mary11k
1

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.

ADD REPLYlink written 6.4 years ago by pengcui198930
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