Table 1.

Summary of the assessment of the three protocols for different input amounts and sample degradation stages

RNA seq Protocol	RNA Input	1 ng	2 ng	5 ng	10 ng	20 ng	100 ng	Conclusion
TruSeq stranded mRNA	Intact	=	+	++	+++	+++	+++	+Works well at low amounts down to 5 ng -Captures polyadenylated RNAs only -Not suited for degraded or highly degraded samples
	Degraded	*	*	*	*	*	++
	Highly deg.	*	*	*	*	*	*
RiboZero stranded RNA	Intact	+	+	++	++	++	++	+Works well over all input amounts +Captures all RNAs (coding & non coding) +Compares well to mRNA protocol +Well suited for degraded samples -Requires higher sequencing depth -Not suited for highly degraded samples
	Degraded	+	+	++	++	++	++
	Highly deg.	*	*	*	−−	−	−
RNA access	Intact	−	=	++	++	++	*	+Performs well on all samples down to 5 ng +Requires less sequencing depth +Suited for degraded and highlydegraded samples -Captures only preselected RNAs and is only available for human samples -Less similar to the other two protocols
	Degraded	−	=	++	++	++	*
	Highly deg.	−−	−	=	+	+	*

A +, ++, or +++ indicates that the protocol performed (very) well on the input, = indicates borderline performance, and a – or – – indicates an unsatisfactory performance. The symbol * is used to indicate input conditions that were not tested