RNA-seq analysis of wild-type HEK293, HEK293 treated with DMSO, ML216 or NSC617145, wild-type mESCs and dhx9KO mESCs

G4s are built by stacked guanine tetrads connected via Hoogsteen hydrogen bonds and can be formed by intra- or inter-molecular folding of the tetramers. R-loops are three-stranded structures which contain a DNA-RNA hybrid and a displaced single-stranded DNA. Both G4s and R-loops are involved in key biological processes, including transcriptional regulation, replication, genomic instability, class switch recombination in B cells, DNA damage and repair, and telomere maintenance. To understand the transcriptional regulation of G4s and R-loops, we performed the RNA-seq analysis on HEK293 cells treated with the inhibitors of G4 resolving helicase ML216 or NSC617145 and mESCs in which the resolving helicase DHX9 of G4 and R-loop was knockout. To investigate the effect of ML216 and NSC617145 in HEK293,we treated HEK293 with corresponding helicase inhibitors and performed RNA-seq. To invistegate the effect of Dhx9 in mESC,we established dhx9 knockout mESC using CRISPR/Cas9 and performed RNA-seq.