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Fig. 4 | Genome Biology

Fig. 4

From: Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets

Fig. 4

5hmCpG mapping by SCL-exo in mouse ES cells. a Venn diagrams indicating the percentage of overlapping id CpGs between two technical replicates of SCL-exo (left diagram) and two technical replicates of TAB-seq (right diagram) in E14 mESCs. SCL-exo id CpGs were selected for having a coverage ≥ 20× and TAB-seq id CpGs for being at least 20 % hydroxymethylated. b Genome-wide correlation coefficient value for two technical replicates of SCL-exo (left panel) and TAB-seq (right panel). Signals were compared for id CpGs with between 20× and 60× coverage in SCL-exo and with between 15 % and 40 % of hydroxymethylation in TAB-seq. c Graph representing the percentage of overlapping CpGs between either SCL-exo and TAB-seq (hydroxymethylation ≥ 20 %) or SCL-exo and Aba-seq (coverage ≥ 20×, 2,320,973 CpGs), as a function of the coverage of SCL-exo id CpGs. For each SCL-exo coverage value a similar number of CpGs were randomly picked among the 21,342,492 CpGs of the mm9 genome, and submitted to the same analysis. d Venn diagrams indicating the percentage of id CpGs from either SCL-exo (called from the consensus.wig file with a threshold (th) of 40×, left diagram) or TAB-seq (hyroxymethylation ≥ 20 %, right diagram), overlapping with hMeDIP-seq peaks (called with a threshold of 20×). e Functional annotation of the SCL-exo and TAB-seq identified 5hmCpGs. Annotation was done with GREAT (http://bejerano.stanford.edu/great/public/html/) and binomial raw p values are given in brackets for each item

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Genome Biology

ISSN: 1474-760X

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