Table 1.

Summary of datasets used.

GEO Accession	GSE53960	GSE41637	GSE84158	GSE70389	GSE58928
Library Type	Single-end	Paired-end	Paired-end	Paired-end	Paired-end
	Unstranded	Stranded (dUTP method)	Unstranded	Stranded	Unstranded
	rRNA depleted but not poly(A) selected	Poly(A) selection	Total RNA	rRNA depleted, total RNA	rRNA depleted, total RNA
Read length	50bp	80bp	100bp	100bp	101bp
# Reads per sample	25–40 million, but 2 replicates were pooled to make 50–80 million	52–80 million	~15 million	37–76 million	142–161 million
# Biological replicates	8	1*	2 MB, 2 MT**	2 MB, 2 MT	1 MB 2 MT
Strain	Fischer 344	BN/SsNHsd (Brown Norway)	C2C12 mouse	C2C12 mouse	C2C12 mouse
Sex	4 female, 4 male	Male	-	-	-
Age	21 weeks	‘Breeding age’	MT – 7 day	MT – 4 day	MT – 4 day
Extra details	Skeletal muscle: gastrocnemius, ~100 mg ground Liver: ~100 mg ground Heart, brain, testis: Whole organ ground	Skeletal muscle: right quadriceps Heart: transmural Brain: visual cortex including grey and white matter Liver: unspecified Testis: Right, transverse section			Control from siRNA experiment, so treated with scrambled siRNA
Reference	(Yu et al., 2014) [54]	(Merkin et al., 2012) [56]	(Doynova et al., 2017) [79]	(Martone et al., 2016) [80]	(Singh et al., 2014) [81]

* There are three biological replicates per tissue, but two are sequenced to a much lower depth with 36nt read length and so were not used in the original paper for splicing analysis, and have been excluded from the present analysis due to MAJIQ’s dependence on junction reads for quantification.

** MB = myoblast, MT = myotube