Supplementary Figure 4: Effect of IgG correction in DIP-seq data.

(a) Schematic visualization of false positive rate for enriched regions. Briefly, false positive rate (FPR) was estimated based on the inverse fraction of regions identified by both Input and IgG versus total regions. (b) Estimated false positive rate of enriched regions using IgG or Input as control for Tdg knockdown mESCs for n = 2 biologically independent samples. Data shown as mean. (c) Estimated false positive rate for individual mESC or MEF datasets. *Estimated based on controls from mESCs. (d) Venn diagram of enriched 5hmC regions in mESCs with different techniques and controls of each n = 1 biologically independent samples. (e, f) Fraction of enriched 5modC regions identified using IgG or Input overlapping repetitive elements (e) and dinucleotide repeats (f) for 5caC n = 2, 5fC n = 2, 5hmC n = 7 and 5mC n = 6 biologically independent samples. Presented as mean ± s.d. P-values calculated using two-tailed T-test. (g) Venn diagram of 5mC and 5hmC overlap using IgG or Input controls (top) and paired line plot of 5mC and 5hmC overlap using IgG or Input controls for multiple studies (indicated by symbols, bottom). Data shown as mean and individual data points of n = 6 biologically independent samples. P-values calculated using two-tailed paired T-test. ▲ = ERP000570, ● = GSE31343, ■ = GSE24841, ▼= GSE42250. (h) GO term enrichment for top genes (n = 500) enriched for 5hmC in mouse embryonic fibroblasts (MEFs) using DIP-seq with either IgG or Input controls. P-values calculated using PANTHER overrepresentation test GO biological processes. (i) Signal track in mESCs of ChIP-seq controls over IgG DIP-seq enriched regions.