Extended Data Fig. 4: Performance comparison of PRAISE data from different biological replicates and KAPA RNA-seq kit.

(a, b) The performance of a new batch of HEK293T cells using Takara v3 library construction. a, Venn plot depicting ~78% overlapping between two technical replicates. b, Correlation of deletion rates of overlapping 2,749 Ψ sites detected in both technical replicates (R² = 0.965). (c) Venn plot depicting the 84.6% overlapping between two biological replicates using Takara v3 library construction. ‘Overlapped sites of 1^st batch’ represents 2,209 Ψ sites originally reported in HEK293T cells, and ‘Overlapped sites of 2^nd batch’ represents 2,749 Ψ sites detected in two technical replicates of 2^nd batch cells. (d) Correlation of deletion rates of overlapped Ψ sites in (c) of two biological replicates (R² = 0.966). (e, f) The performance of a new batch of HEK293T cells using KAPA library construction kit (KAPA Stranded RNA-Seq Kit, #kk8400). e, Venn plot depicting the ~86% overlapping between two technical replicates. f, Correlation of deletion rates of 2,055 Ψ sites detected in two technical replicates (R² = 0.980). (g) Venn plot depicting the 67.5% overlapping between two biological replicates using Takara v3 library construction and KAPA kit. ‘Overlapped sites of 1^st batch’ represents originally 2,209 Ψ sites reported in HEK293T cells, and ‘Overlapped sites of 3^rd batch’ represents 2,055 Ψ sites detected in two technical replicates of 3^rd batch cells. (h) Correlation of deletion rates of overlapped Ψ sites in (g) between two biological replicates (R² = 0.959).