ChIP-seq analyses of RUNX1 and TET2. (A) A ZENBU browser screenshot showing a typical relationship between RUNX1 and TET2 ChIP-seq data, and the methylation level. The DNA methylation track is the M-value measured by the methylation array. Green and purple bars represent positive and negative M-values, respectively. ChIP-seq tracks show the tpm. (B) Overlap between RUNX1 (blue) and TET2 (red) ChIP-seq peaks. (C) Distribution of TET2 ChIP-seq reads around RUNX1 ChIP-seq peaks. The x- and y-axes indicate ±3-kbp genomic region from RUNX1 ChIP-seq peaks and read count per million mapped read, respectively. The solid line and shaded area render average and standard error of read count per million mapped reads. The experiment was done in 2 biological replicates. (D) Distribution of TET2 ChIP-seq reads around RUNX1 ChIP-seq peaks in RUNX1-knockdown Jurkat (RUNX1_shRNA [short hairpin RNA], green line) and negative control (NC_shRNA, red line). The x- and y-axes indicate ±3-kbp genomic region from the summit of RUNX1 ChIP-seq peaks and read count per million mapped read, respectively. The solid lines and shaded area render average and SD. The experiment was done in 2 biological replicates. (E) Total read count per million mapped read at ±3000-bp regions from RUNX1 ChIP-seq peaks. Red and green bars represent NC shRNA transduced Jurkat cells (NC_shRNA) and RUNX1-knockdown Jurkat cells (RUNX1_shRNA), respectively. Error bars represent SD. The asterisk denotes P < .05. The experiment was done in 2 biological replicates. (F-G) Distribution of RUNX1 and TET2 ChIP-seq reads around TSSs (±3 kb) (F) and CpG islands (CGI; ±3 kb) (G). The color key represents read counts per million. (H) Scatter plots showing relation between M-value and ChIP-seq peak heights of RUNX1 (top), TET2 (middle), and RUNX1 at regions with both RUNX1 and TET2 (bottom, RUNX1 at intersection). x- and y-axes represent M-value and −log₁₀q value, respectively. The scatterplots are represented as blue smoothed shade density.