Tao 2011, H3K4me3 in Lsh WT and Lsh-/- MEFs, GSE29393


High-resolution cytosine methylation map of the murine genome modulated by Lsh, a chromatin remodeling family member that has previously been shown to regulate CpG methylation at repetitive sequences. Lsh also controls genome-wide cytosine methylation at nonrepeat sequences and relate those changes to alterations in H4K4me3 modification and gene expression.


Data downloaded from GEO series: GSE29393
Input file format: SRA


From M. musculus (July 2007 NCBI37/mm9).

Filename Description Feature GEO-ID
1 H3K4me3_wt.sga MEF(Lsh+/+) H3K4me3 H3K4me3 GSM726806
2 H3K4me3_Lsh_ko.sga MEF(Lsh-/-) H3K4me3 H3K4me3 GSM726807

Technical Notes

The SGA files were gerenerated from GEO accessory text files provided in Eland export format. Mapped sequence reads with alignment scores lower than 10 were discared. The source genome coordidnates were remapped from mouse genome assembly Feb. 2006 (NCBI36/mm8) to July 2007 (NCBI37/mm9) using the liftOver software from UCSC.


  1. Tao Y, Xi S, Shan J, Maunakea A, Che A et al.
    Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences. Proc Natl Acad Sci U S A 2011 Apr 5;108(14):5626-31. PMID: 21427231

  2. GEO series GSE29393 H3K4me3 modification analysis comparing Lsh WT and Lsh-/- MEFs.