Refined RIP-seq protocol for epitranscriptome analysis with low input materials
Fig 1
Low/high salt-washing method outperforms competitive elution method.
(A) Schematic diagram of 3 strategies of m6A MeRIP. (B) S/N ratio of GLuc/CLuc was highest in Method II using low/high salt washing. An RNA mixture containing equal amounts of the m6A modified control RNA GLuc, the unmodified control RNA CLuc, and NEB antibody were used for m6A MeRIP. (C) S/N ratio of GLuc/CLuc was further increased in a second round of IP using Method II. S/N ratio of GLuc/CLuc (panel D) and SETD7/GAPDH (panel E) in 3 replicates of 1 round of IP. Data related to this figure can be found in S1 Data. CLuc, unmodified control RNA; GLuc, m6A-modified control RNA; IP, immunoprecipitation; m6A, N6-Methyladenosine; m6A MeRIP, m6A RNA immunoprecipitation followed by high-throughput sequencing; NEB, New England Biolabs; S/N, signal-to-noise.