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5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

Hume Stroud1, Suhua Feng12, Shannon Morey Kinney3, Sriharsa Pradhan3 and Steven E Jacobsen12*

Author Affiliations

1 Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA

2 Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA

3 New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA

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Genome Biology 2011, 12:R54  doi:10.1186/gb-2011-12-6-r54

Published: 20 June 2011

Additional files

Additional file 1:

Supplementary figures and table. Figure S1: 5hmC dot blots on oligos with varying amounts of 5hmC. Figure S2: characterization of defined 5hmC peaks. Figure S3: correlation of 5hmC and gene expression. Figure S4: 5hmC and different classes of putative enhancers [12]. Figure S5: gene ontology analysis of genes that overlap with 5hmC peaks [13]. Figure S6: genome-browser views of 5hmC, enhancers and TFBSs [9,14,15]. Figure S7: sequence composition over 5hmC regions in different genomic locations. Table S1: primers used for quantitative PCR.

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