Lister 2009, human DNA methylomes (BS-Seq)

Description

First genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors.

Source

Data downloaded from http://neomorph.salk.edu/human_methylome/

(click on "Download Data" then "Methylcytosines")

Samples

From Human Mar. 2006 (NCBI36/hg18) Assembly

Filename Description Feature GEO-ID
1 H1_meth.sga H1 Meth(+) Meth -
2 H1_meth_r1.sga H1 Meth(+)/rep1 Meth -
3 H1_meth_r2.sga H1 Meth(+)/rep2 Meth -
4 IMR90_meth.sga IMR90 Meth(+) Meth -
5 IMR90_meth_r1.sga IMR90 Meth(+)/rep1 Meth -
6 IMR90_meth_r2.sga IMR90 Meth(+)rep2 Meth -
7 H1_dmeth.sga H1 Meth(-) DMeth -
8 H1_dmeth_r1.sga H1 Meth(-)/rep1 DMeth -
9 H1_dmeth_r2.sga H1 Meth(-)/rep2 DMeth -
10 IMR90_dmeth.sga IMR90 Meth(-) DMeth -
11 IMR90_dmeth_r1.sga IMR90 Meth(-)/rep1 DMeth -
12 IMR90_dmeth_r2.sga IMR90 Meth(-)/rep2 DMeth -

Technical Notes

The sga files were gerenerated from tab-delimited text files available from the URL indicated above. These files provide the ratio of methylated versus non-methylated C-residues in the human genome assembly Mar. 2009 (NCBI36/hg18). Two sga files were generated from each experiment providing the coordinates of "methylated" and "demethylated" (methylation-depleted) C residues, respectively. Only C-residues that occur in a CpG context were considered. A C-residues was considered "methylated" if at least 50% of the reads covering the residue indicated methylation.

References

  1. Lister R, Pelizzola M, Dowen RH, Hawkins RD et al.
    Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19;462(7271):315-22. PMID: 19829295

Genome browser viewable files

   IMR90 Meth(+)   http://epd.vital-it.ch/bigWIG/hg18/meth.BW    
   IMR90 Meth(-)   http://epd.vital-it.ch/bigWIG/hg18/dmeth.BW