Table 1.

Minion direct-cDNA runs included in this study

Exp name	Primer for 2nd strand synthesis	Basecalled reads	Genome mapping	Transcriptome mapping			Strand bias
			Alignments	Alignments	Genes	Isoforms	Sense	Antisense
SSP_1	SSP	1,067,062	926,986	856,699	12,661	19,079	1.8%	98.2%
SSP_2		372,188	302,164	265,555	12,586	18,351	2.4%	97.6%
SSP_3		428,451	269,505	215,150	11,790	17,426	6.0%	93.0%
SSP_4		805,214	563,132	329,046	15,078	22,808	6.2%	93.8%
SSP_5		203,384	122,662	75,874	9858	13,416	3.7%	96.3%
SSP_6		2,698,484	2,003,969	520,347	12,558	19,710	6.7%	92.3%
SL1_1	SL1	7,811,076	6,776,420	6,015,856	15,080	24,474	26.7%	73.3%
NP_1	None	330,272	149,490	106,081	6736	8914	1.8%	98.2%
NP_2		3,238,319	2,666,799	1,962,645	13,041	20,486	1.7%	98.3%
NP_3		630,506	514,711	398,165	9781	14,107	1.4%	98.6%
NP_4		99,031	77,991	54,418	5343	6890	1.6%	98.3%
NP_5		575,203	456,843	353,154	9681	14,298	1.6%	98.4%

SSP Strand Switching Primer, SL1 SL1 primer, NP no primer.

Reads from all three conditions were combined for the spliced leader analyses below. More details are provided in Supplementary Tables 1 and 2.