Stadler 2011, mouse DNA methylomes (BS-Seq)

Description

Genome-wide, single-base-resolution maps of methylated cytosines in mouse, from both embryonic stem cells (ES) and derived neuronal progenitors (NP).

Source

Data downloaded from GEO (GSE30202) for ES cell and NP cell

Samples

From Mouse Jul. 2007 (NCBI37/mm9) Assembly

Filename Description Feature GEO-ID
1 GSE30202_BisSeq_ES_CpGDmeth.sga ES Meth(-) DMeth GSM748786
2 GSE30202_BisSeq_ES_CpGmeth.sga ES Meth(+) Meth GSM748786
3 GSE30202_BisSeq_NP_CpGDmeth.sga NP Meth(-) DMeth GSM748788
4 GSE30202_BisSeq_NP_CpGmeth.sga NP Meth(+) Meth GSM748788

Technical Notes

The sga files were gerenerated from tab-delimited text files available from the URL indicated above. These files provide the total number of read and non-methylated reads that map to C-residues in the mouse genome assembly mm9. 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. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, Oakeley EJ, Gaidatzis D, Tiwari V, Schubeler D
    DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011 Dec 14;480(7378):490-5. PMID: 22170606