Extended Data Fig. 2: Quantification of gradual gDNA restriction and GPSeq reproducibility.

(a) Distribution of the position of the peak in the YFISH fluorescence intensity radial profile (see Extended Data Fig. 1c) at different restriction times, in two HindIII experiments (Exp.1 and 2). (b) Same as in (a), but for the position of the inflection point. (c) Distribution of the absolute residuals of the linear regression fitting between the log2 GPSeq score (1 Mb resolution, overlapping windows with 100 kb step size) in two HindIII experiments (Exp.1 and 2). The regression layers were generated by dividing the linear regression line into 10 bins of equal size. (d) Same as in (c) but correlating the GPSeq score at 100 kb resolution. All box plots in (c, d) span from the 25^th to the 75^th percentile and whiskers extend from –1.5×IQR to +1.5×IQR from the closest quartile, where IQR is the inter-quartile range. Dots: data falling outside whiskers. (e) Gradual gDNA digestion with MboI revealed by wide-field epifluorescence microscopy. Green: MboI cut sites. Blue: DNA stained with Hoechst 33342. Scale bars: 20 µm (field-of-view) and 10 µm (insets). Times indicate the duration of incubation with MboI. Mid optical sections are shown. The same dynamic range was used for all the digestion times. The experiment was repeated twice with similar results. (f, g) Same as in (a, b), but for MboI experiments (Exp.3 and 4). (h) Correlation between the GPSeq score in four GPSeq experiments at chromosome resolution (that is, using genomic windows of the size of each chromosome). (i) Same as in (h) but at 1 Mb resolution (overlapping windows, 100 kb step size). (j) Same as in (h) but at 100 kb resolution (non-overlapping windows). In all the violin plots in the figure, the median is shown as a black line and the violins extend from the min to the max value. Sample size information for (a-d), (f, g) and (i, j) is available in Supplementary Table 11. All the source data for this figure are from HAP1 cells.