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A comparative analysis of DNA methylation across human embryonic stem cell lines

Pao-Yang Chen12, Suhua Feng1, Jong Wha Joanne Joo3, Steve E Jacobsen145* and Matteo Pellegrini156*

Author Affiliations

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

2 Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA

3 Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, CA 90095, USA

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

5 Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA

6 Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA

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Genome Biology 2011, 12:R62  doi:10.1186/gb-2011-12-7-r62

Published: 6 July 2011

Additional files

Additional file 1:

Supplementary information. Includes supplementary Table S1 and Figures S1 to S14.

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Additional file 2:

Supplementary Table S2. List of genes associated with differentially methylated CpG islands.

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Additional file 3:

Supplementary Table S3. List of the 1,020 genes that are predicted to have allele-specific expression.

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Additional file 4:

Supplementary Table S4. List of 75 imprinted genes from the literature.

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Additional file 5:

Supplementary Table S5. List of the 110 genes that are enriched with differentially methylated CG sites in at least one cell line.

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Additional file 6:

Supplementary Table S6. List of motifs in transcription factors and the correlation coefficients between change of methylation and the associated changes of gene expression at their binding sites, and at the neighboring sequences.

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Additional file 7:

Supplementary Table S7. List of differentially methylated regions overlapped across the three HESC lines.

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