I would like to analyze Chip-seq ES cells data for Oct4/Sox2/Nanog sequenced to 36bp or longer with Illumina GA2 or HiSeq2000. For what I found in the public archives, there are some 1-3 year old data sets that are not homogeneous in read length, some of them being 36bp but others being as short as 26bp.
Does anybody know of the existence of such datasets that are public or will be public in the near future and I could use?
So far I have only found data sets shorter than 36bp or data sets that don't include the three factors from the same sample (e.g., Oxt4/Nanog but no Sox2).
•
written
by
Ahdf-Lell-Kocks •
what public archives are you looked through?
It doesn't seem hard to find on SRA:
I like the simple search interface for ddbj but you can also use GEO.
You can also try the RoadMap Epigenomics Project
Thanks. It seems the RoadMap Epigenomics Project has histone modifications and DNA methylation data, but not TFs like Oct4/Sox2/Nanog.
Log in to answer this question.
May I ask why you don't want to use the ones with sub-36 bp read lengths? Probably there is not much other data out there because doing ChIP-seq can be pretty challenging and why redo the experiment with a longer read length when ES ChIP-seq profiles for these factors are already available?