Open Access Highly Accessed Research article

Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions

Bo Wen14, Hao Wu2, Yuin-Han Loh3, Eirikur Briem1, George Q Daley3 and Andrew P Feinberg1*

Author Affiliations

1 Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

2 Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA

3 Division of Pediatric Hematology/Oncology, Children's Hospital Boston and Howard Hughes Medical Institute, Boston, MA, USA

4 Current address: Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China

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BMC Genomics 2012, 13:566  doi:10.1186/1471-2164-13-566

Published: 26 October 2012

Additional files

Additional file 1:

Table S1. Description: Genome coverage and average size of LOCKs in human PSCs and differentiated cells.

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Additional file 2:

Figure S1(A-D). Description: qRCR validation of H3K9me2 ChIP-chip data on 23 loci. Upper panels show log2 (ChIP/Input) ratios of microarrays and green bars denote regions selected for qPCR validation; lower panels present qPCR enrichments of ChIP over input in the selected regions.

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Additional file 3:

Figure S2. Description: LOCKs overlap partial methylation domains (PMDs). (A) One representative region (on chromosome 17) where LOCKs and PMDs overlap, green and orange bars show locations of LOCK (green) and PMD (orange), and hypomethylation blocks (purple), respectively; (B) H3K9me2 density in and out of PMDs. X-axis is the probe log2 ratios between ChIP and control samples. Y-axis is the the probability density.

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Additional file 4:

Table S2. Description: Coordinates of EIs (HG18).

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Additional file 5:

Figure S3. Description: Average H3K9me2 densities in EIs and their adjacent regions.

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Additional file 6:

Figure S4. Description: H3K9me2 ChIP-chip experiments in whole genome (WG) and replicate (rep) arrays.

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Additional file 7:

Figure S5. Description: Nucleosome density in EIs and adjacent regions. We compared common EIs of HA, HAEC and HPF with nucleosome maps of GM12878 (Supplementary Table S3), to overcome potential lineage specificity among those cell types.

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Additional file 8:

Figure S6. Description: Flow diagram of EI detection.

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Additional file 9:

Table S3. Description: Public datasets used for analysis.

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Additional file 10:

Table S4. Description: qPCR primer sequences.

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