Systematic evaluation of spa-ChIP-seq with comparison to manual workflow, cross-linking conditions, and buffer compositions. (A,B) Scatterplots comparing normalized read counts (log₂) between automated and manual ChIP-seq samples (A) and automated replicates (B) at H3K27ac or H3K27me3 shared peaks. (C,D) Scatterplots of read counts (log₂) on shared peaks, IGV (Robinson et al. 2011) tracks, and heatmaps of ±5 kb from the center of transcription start sites (TSSs) or peaks showing the automated ChIP-seq results of H3K27ac (C) and H3K27me3 (D) for evaluating cross-linking conditions, DSG+FA versus FA only (top), and buffer compositions, EBB versus LB3 (bottom). The Pearson r correlation coefficients are reported on the lower right corner of the scatterplots. A total of 32 ChIP-seq experiments were performed, 16 of them using spa-ChIP-seq and 16 of them using manual ChIP-seq, with additional data in Supplemental Figure S2.