Table 2. Summary of SQANTI3 analysis of IsoSeq data.

In-depth characterisation of isoforms in control and Exp+ long-read RNA-seq data utilising SQANTI3 pipeline following stringent quality control. SQANTI3 subdivides splice junctions into known (present in reference transcriptome) and novel (not in reference transcriptome). Canonical splice junctions refer to the most common type of splice junction (GTAG, GCAG, ATAC)), while non-canonical refers to other rarer and tissue specific splice junctions with different donor and acceptor sites. SQANTI3 defines novel as genes or splice junctions that are absent from the reference transcriptome.

	Control (n = 4)		Exp+ FECD (n = 3)
Genes	2,318		4,652
Isoforms	3,113		8,032
Gene Classification
	# of genes		# of genes
Annotated Genes	2,309		4,642
Novel Genes	9		10
Splice Junction Classification
	# splice junctions	Percent	# splice junctions	Percent
Known canonical	27,552	97.18	52,153	97.35
Known non-canonical	1	0.00001	21	0.04
Novel canonical	798	2.81	1,400	2.61
Novel non-canonical	0	0	0	0