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Series GSE11034 Query DataSets for GSE11034
Status Public on Jul 06, 2008
Title Genome-scale DNA methylation maps of pluripotent and differentiated cells
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps covering the vast majority of CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for murine embryonic stem (ES) cells, ES-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of ES-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumors. More generally, the results establish RRBS as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
Keywords: High-throughput Reduced Representation Bisulfite Sequencing (RRBS), Illumina, cell type comparison
Overall design Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) of 18 murine cell types.

Raw sequence data files for this study are available for download from the SRA FTP site at
Contributor(s) Mikkelsen TS, Meissner A, Gu H, Gnirke A, Jaenisch R, Lander ES
Citation(s) 18600261
Submission date Apr 02, 2008
Last update date May 15, 2019
Contact name Tarjei S Mikkelsen
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL6677 Broad-Mouse-Illumina-Genome-Analyzer-RRBS
Samples (18)
GSM278889 TcellCD8_RRBS_MspI
GSM278890 Astro_primary_p11_RRBS_MspI
SRA SRP000179
BioProject PRJNA107127

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Supplementary file Size Download File type/resource
GSE11034.README.txt 740 b (ftp)(http) TXT
GSE11034_RAW.tar 11.6 Gb (http)(custom) TAR (of TXT)
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Processed data provided as supplementary file

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