最显著的RNA修饰物- N6-甲基腺嘌呤(m6A)- 可影响基因调控和癌症进展。然而，m6A在长非编码RNA(lncRNA)中的程度和影响仍不清楚。目前最成熟的m6A检测方法是甲基化RNA免疫沉淀和测序(MeRIP-seq)。然而，牛津纳米孔技术最近开发了直接RNA测序(dRNA-seq)方法，可在更高分辨率和本地形式下进行m6A识别。我们对U87-MG胶质母细胞瘤细胞系进行了整个转录组测序，使用MeRIP-seq和dRNA-seq两种方法。对于MeRIP-seq，使用nf-core/chipseq来鉴定m6A peak，对于dRNA-seq则使用EpiNano流程。 MeRIP-seq分析识别出5086个lnRNA转录本，而dRNA-seq则从中识别出336个lnRNA转录本，其中有556个和198个被发现是m6A修饰的。同时也有24个m6A重叠的lncRNAs。Gliovis数据库分析表明，识别出的重叠lncRNAs的大部分表达与胶质瘤分级或患者生存预后相关。我们发现，在所提供的24个修饰的lncRNAs清单中，m6A出现的频率差异超过9倍。MIR1915HG，THAP9-AS1，MALAT1，NORAD1和NEAT1（49-88nt）的m6A频率最高，而MIR99AHG，SNHG3，LOXL1-AS1和ILF3-DT的m6A频率最低（445-261nt）。综上所述，(1)我们提供了一个高精度的U87-MG细胞中24个m6A修饰的lncRNAs清单; (2)我们总结出，由于其更高的lncRNA覆盖范围，MeRIP-seq更适合进行m6A筛选研究，而当需要更深入的m6A数量和精确位置分析时，dRNA-seq最有用。本文缩写：(dRNA-seq)直接RNA测序，(GBM)胶质母细胞瘤，(LGG)低级别胶质瘤，(lncRNAs)长非编码RNA，(m6A)N6-甲基腺嘌呤，(MeRIP-seq)甲基化RNA免疫沉淀和测序，(ncRNA)非编码RNA，（ONT）牛津纳米孔技术，(Lietuvos Mokslo Taryba)立陶宛科学委员会。

The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent 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 Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing 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, respectively. 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 the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.