Figure 1

Characterisation of bulk G4-CUT&Tag. (a) Schematic diagram of G4-CUT&Tag workflow. Fixed permeabilised cells are incubated with the G4 structure-specific BG4 single-chain variable fragment (scFv), followed the secondary antibodies, and then adapter-loaded proteinA-Tn5 to enable the integration of adapters at G4 target loci for next-generation sequencing library preparation. (b) Example genome browser view of G4-CUT&Tag signals and G4 peaks called obtained from 100,000 K562 (red) and 100,000 U2OS (blue) cells with comparisons to published G4-ChIP-seq data²¹ (pink, light blue respectively), and sites that fold into G4 structures in vitro (called observed quadruplex sequences OQs, orange)²⁰ Light grey shading highlights G4 peaks in the MYC locus. Gene annotations are shown in black below. (c) Hierarchical clustering of the Spearman correlation matrix for G4-CUT&Tag replicates. G4-CUT&Tag was performed on three biological replicates (b1, b2, b3) with two technical replicates (t1, t2) for 100,000 K562 and 100,000 U2OS cells. Spearman correlations between samples were computed at G4 peaks on read coverage normalised to library size. (d) Venn diagram showing the number of G4 peaks and their overlap from 100,000 (100 k), 50,000 (50 k) and 10,000 (10 k) K562 cells.