Extended Data Fig. 1: Validation of Paired-Damage-seq.
From: Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability
a, Dotplots showing the relative enrichments of model DNA sequences treated with different buffer conditions. Nickases Nt.AlwI and Nt.BstNBI were used to generate SSBs as positive control; technical replicates n = 3 for all conditions. b, Line plots showing the normalized DNA signal enrichments of ATAC-seq, non-targeting tagmentation control and Paired-Damage-seq DNA signal on DHSs (DNase I hypersensitive sites) of HeLa cells. c, Barplots showing the relative DNA damage levels (normalized by spike-in mouse 3T3 cells) in HeLa cells labeled with different enzyme combinations; technical replicates n = 3 for all combinations. d, Scatter plot showing the correlation between detected DNA damage reads densities and the numbers of Nt.BbvCI cutting sites per 10k-bp non-overlapping bins for control nuclei. e, Scatter plots showing the fraction of RNA reads mapped to human and mouse reference genome for each cell barcode in the species-mixing experiment. Barcodes with less than 75% reads from the same species were identified as mixed cells. f, Scatter plots showing the Pearson’s correlation coefficient of Paired-Damage-seq RNA dataset with in-house generated nucleus RNA-seq from HeLa cells. g, Scatter plots showing the Spearman’s correlation coefficients of pair-wise correlations between bulk and aggregated single-cell Paired-Damage-seq DNA dataset, AP-seq (AP-sites) and CLAPS-seq (8-Oxoguanine) datasets from HeLa cells. ATAC-seq and non-targeting tagmentation control are also shown for comparisons.
