Homo sapiens Raw sequence reads

The most prominent RNA modification - N6-methyladenosine (m6A) affects gene regulation and cancer progression. The extend and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Tech- nologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identifica- tion at higher resolution and in its native form. We performed whole transcriptome sequenc- ing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP- seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respec- tively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs, varied more than 9-fold throughout provided list of 24 modi- fied lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MA- LAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt)