Supplementary Figure 5: In vitro ChIP-seq scrambling experiments with site-specific histone PTM antibodies confirm the integrity of the library.

(a) The linear range of the downstream DNA processing was confirmed by subjecting 10 pg of the standard DNA mixture containing 4 BC-601 sequences equipped with a unique barcode each (combined at a ratio of 1:10:100:1000 eq for standards A, B, C, D; see Materials and Methods) to the identical multiplex PCR and Ion Torrent next generation sequencing conditions as for the library in vitro ChIP-Seq exeriments described later. Plotting of the obtained raw DNA reads (log-log display), averaged from 3 independent PCR/sequencing experiments, showed both an excellent reproducibility of the data (power law curve fit, R² value = 0.9992) and the preservation of the DNA ratios in the sequencing range typically employed in the current study. (b-d) Analysis of DNL-1 stability towards histone exchange. 12 fmoles of total NUCs were combined with an α-H3K9ac (b), α-H4K8ac (c) or α-H3K4me3 (d) antibody. (e) The experiment was identical as in (d), except this NUC library had been stored for > 6 months at 4 °C. All downstream processing was performed as described for Supplementary Fig. 4. Internal normalization was performed to the following variants (set as 1, red asterisks): H3Kac₅ (b), H4Kac₅ (c), or H3K4me3 (d,e). Values are shown as (mean ± SD, n=3) for (c,d) or plotted separately for (n=2, b,e) employing the same grid as in Fig. 1b.