Extended Data Fig. 4: Estimating the resolution and error of ENTRAP-seq using empirical noise distributions.

(a) Distribution of Δ values in the 2000 tile viral library where Δ is defined as the difference in enrichment of a given tile between two biological replicates. The dashed red line indicates 2 empirical standard deviations in Δ values. (b) Resolution in one replicate: The distribution in (a) is used as a null distribution to estimate the measurement error, defined as 2σ. This 2σ value corresponds to the 95% confidence interval for the Δ between tiles that are not different in strength. Hence, the minimal detectable Δ with p ≤ 0.05 is defined as Δ larger than 2σ. The plot shows this detectable Δ as a function of the number of tiles passing a library coverage cutoff in the 2000 tile library (as in Fig. 3c) (see Supplementary Text for calculation details). (c) Distribution of residuals in the 2000 tile viral library, defined as the orthogonal distance of the enrichment value of a given tile with respect to the the rep1 = rep2 (y = x) line (see Supplementary Text for details). The dashed red line indicates 2 empirical standard deviations in residual values. (d) Resolution using two replicates: The distribution in (c) is used as a null distribution to estimate the error of comparing the mean enrichment between two tiles, defined as 2σ. This 2σ value corresponds to the 95% confidence interval for the difference between the mean enrichment of two tiles that are not different in strength. Hence, the minimal detectable enrichment difference in two replicates with p ≤ 0.05 is defined as difference larger than 2σ residuals. The plot shows this detectable difference as a function of the number of tiles passing a library coverage cutoff (as in Fig. 3c) (see Supplementary Text for calculation details). (e) Resolution is independent of enrichment. For each tile, the residuals were calculated as in (c) and plotted against the mean enrichment of that tile. (f) Assessment of data heteroscedasticity. Tiles in (e) were binned according to their enrichment and, for each bin, the standard deviation in residual values was calculated (y-axis). The s.d. of residuals hovers around 0.2 for all bins, showing that residuals are similarly variable across the enrichment dynamic range.