Prolonged Sample Storage Reshapes the m⁶A Methylation Landscape Through RNA Degradation

N⁶-methyladenosine (m⁶A) is the most common internal modification in eukaryotic mRNA, essential for post-transcriptional regulation. MeRIP-seq is widely used for m⁶A profiling, but RNA degradation challenges accurate analysis. While the effects of sample handling on RNA are known, the impact of tissue sample storage durations on m⁶A remains unclear. We investigated how sample storage durations (0, 2, 12, 24, and 48 h at room temperature) affect RNA integrity, m⁶A peaks, and transcriptomes in mouse liver. RNA integrity declined with time, reducing m⁶A peak number and reproducibility. Prolonged storage diverged m⁶A profiles, increased unreported peaks, shifted RRACH motifs, and redistributed peaks to intergenic/intronic regions. Integrated data showed opposing changes in m⁶A and expression for some genes, suggesting storage degradation confounds epitranscriptomic interpretation. Sample storage durations are critical for m⁶A accuracy, emphasizing the need for standardized handling in MeRIP-seq studies.