Fig. 1: Overview of ssG4-seq method.
From: ssG4-seq for global profiling of strand-specific G-quadruplex structures in mammalian genomes
a Schematic diagram of ssG4-seq method. Key steps include G4 immunoprecipitation using the BG4 antibody, double-stranded DNA digestion by DSN nuclease, construction of single-strand-specific libraries, and deep sequencing. Pink dots indicate nucleotide modifications in linkers. b Pearson correlation analysis showing high reproducibility between three ssG4-seq biological replicates (Rep) in K562 cells. c IGV snapshot of G4 signal in K562 cells. Shaded regions represent high-confidence peaks detected by ssG4-seq. d Comparison of FRiP scores across G4 mapping methods. Each data point represents a biological replicate, except for the G4 CUT&Tag-Li data, which is from a single replicate. Error bars represent mean ± s.d. P-values were determined by a two-tailed unpaired Student’s t-test. e ssG4-seq (right) showing a higher signal-to-noise ratio compared to BG4 ChIP-seq (left). f Venn diagram showing the overlap between BG4 ChIP-seq and ssG4-seq peaks. BG4 ChIP-seq specific peaks, n = 420; ssG4-seq specific peaks, n = 6122. g ssG4-seq (pink) showing higher signal around overlapped peaks, ssG4-seq-specific peaks, BG4-ChIP-specific peaks compared to BG4 ChIP-seq (blue). Randomly selected genomic regions serve as a negative control.
