This article is part of a special issue on epigenomics.

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Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Patrick Boyle1, Kendell Clement1234, Hongcang Gu1, Zachary D Smith123, Michael Ziller123, Jennifer L Fostel1, Laurie Holmes1, Jim Meldrim1, Fontina Kelley1, Andreas Gnirke1 and Alexander Meissner123*

Author Affiliations

1 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

2 Harvard Stem Cell Institute, Cambridge, MA 02138, USA

3 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA

4 Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA

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Genome Biology 2012, 13:R92  doi:10.1186/gb-2012-13-10-r92

Published: 3 October 2012

Additional files

Additional file 1:

Figures S1 to S6. Figure S1: schematic of the mRRBS protocol. Figure S2: gel images from MspI digested DNA and final pooled libraries. Figure S3: schematic of the dark sequencing approach. Figure S4: pairwise correlation of single-CpG methylation data between technical replicates at different read depths. Figure S5: breakdown of repeat elements captured by mRRBS reads. Figure S6: assessment of rate of chimerism during PCR amplification of barcoded RRBS libraries.

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Additional file 2:

Supplementary Table 1. Summary of sequencing results, conversion rates and CpG methylation coverage as well as details for the RRBS versus mRRBS comparison.

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