Extended Data Fig. 7: Quality control and validation of scEdU–seq analysis.
From: CFAP20 salvages arrested RNAPII from the path of co-directional replisomes
a, Coefficient of Variation (y axis) versus average reads per bin (x axis) for all single-pulse scEdU–seq cells. Each dot is a single cell and the shaded area between two straight lines contain selected cells for subsequent analysis. b, Pearson correlation matrix of replication timing for each pseudo-bulk and WT and CFAP20-KO over three S-phase fractions (early, mid and late), number and colours indicate Pearson correlation c, Dimensionally reduced distance between single cells by UMAP for WT and CFAP20-KO cells. Each dot is a single cell, dots are coloured by S-phase progression or DNA content (based on DAPI). d, DNA content (DAPI, y-axis) versus S-phase progression (x-axis) based on scEdU–seq signal (single EdU pulse for 15 min) from WT and CFAP20-KO cells. The line indicates the fit for a linear model and the ribbon indicates the 95% standard error for the fit. e, Quantification of inter-origin-distance for the indicated cell lines and conditions used to calculate origin firing in Fig. 5b. Each coloured circle represents 1 fibre. Each black circle represents the median of an independent experiment (>100 fibres). The black lines represent the mean of all independent experiments. Statistical significance between WT and the indicated conditions was determined by one-way ANOVA analysis after Dunnett’s correction for multiple testing. P-values shown are respectively 0.0160, 0.8523, 0.0073, 0.8815. f, Heat map comparison of binned IZ timing (left, log2) and IZ efficiency (right, log2) for WT (y-axis) and CFAP20-KO (x-axis) RPE1 cells. Blue dashed line indicates the IZ efficiency in WT while continuous blue line indicates IZ efficiency in CFAP20-KO cells. g, Replication forks per cell for each individual chromosome quantified from the scEdU–seq experiment WT (y-axis) and CFAP20-KO RPE1 cells.
