Figure 3

Validation of small-scale transcription factor ChIP-seq. (A) Profiles generated from 300 pg CEBPA ChIP-DNA. Region spanning a 100 kb region on chromosome 4. (B) Genomic distribution of top 26,713 CEBPA peaks (fold 30 cut-off) from GMP-blasts compared with 7,660 CEBPA peak positions in hepatocytes (fold 30 cut-off, data from [21]), rounded numbers. (C) CEBPA coverage tracks from GMP-blast and hepatocyte gene loci of shared, specific liver or myeloid cell expression. See text for full gene names. (D) De-novo motif search output from MEME (upper panel), and top match JASPAR motif CEBPA (MA0102.2), both in logo format (lower panel). Data set as in D. (E) Distribution of the top match motif CEBPA (MA0102.2, grey) in 200 bp regions centered on CEBPA-1 peak summits. USF1 (MA0093.1, purple) included for comparison. (F) Phylo-P conservation plots in 100 bp (upper panel) and 600 bp (lower panel) regions centered on CEBPA-motifs in CEBPA-1 peaks. Green lines delineate motif position. (G) Quantitative comparison of mean read coverage of two ChIP-seq repeats, CEBPA-1 and CEBPA-2, using CEBPA-1 peak regions defined by MACS2. Quantile normalized, 1/1 diagonal indicated by dashed line (r = pearson correlation coefficient, calculated on normalized data, 1 outlier pre-filtered). MACS2 peak boundaries for CEBPA-1 (H) SeqMiner cluster heatmaps showing signal intensities for CEBPA-1 and CEBPA-2 profiles in 10000 bp regions centered on peak summits. For F and G, peak set as in B.