. 2022 Dec 2;12(12):2010. doi: 10.3390/life12122010

Table 4.

Transcriptome and epitranscritome profiling through applications based on RNA-seq.

Transcriptomics/ Epitranscriptomics	Technology	Application	References
Fusion transcripts	NGS	WTS, TS	[157,158,159]
Fusion transcripts	TGS	SMRT-seq, Direct RNA-seq	[160]
Alternative splicing	NGS	RNA-seq, targeted RNA sequencing	[161,162]
Alternative splicing	TGS	Direct RNA-seq, WTS	[160,163]
mRNA polydadenylation	NGS	3′ enriched RNA seq, 3′ mRNA seq, PAT-seq, Poly(A) ClickSeq	[164,165,166,167]
mRNA polydadenylation	TGS	Full length mRNA seq, FLAM-seq, Long read cDNA-seq	[168,169]
ncRNAs/lncRNAs	NGS	scRNA-seq, WTS, WES, AQRNA-seq, ncPRo-seq, miRNA-seq	[170,171,172,173]
ncRNAs/lncRNAs	TGS	Nanopore-induced phase-shift sequencing (NIPSS)	[86]
m⁶A	NGS	Transcriptome-wide m⁶A seq, m⁶A-RIP seq, m⁶A-REF seq	[174,175]
m⁶A	TGS	Direct RNA-seq	[176]
m⁵C	NGS	RNA-BisSeq, RIP-seq, MeRIP-seq, m5C-RIP seq, AZA-IP seq	[153,154,155,177]
m⁵C	TGS	Direct RNA-seq	[178]
Ψ	NGS	Pseudo-seq	[156]
Ψ	TGS	Direct RNA-seq	[179]
m¹A	NGS	ARM-seq, m¹A-quant seq, m¹A-seq	[180,181,182]