Table 1.

Overview of the protocols used in this study

kit used	protocol	modifications
Illumina TruSeq	TS1	none: standard conditions
	TS2	HD adapters used instead of Illumina adapters
	TS3	3′ adapter ligation 16 °C o/n in the presence of PEG
	TS4	HD adapters used instead of Illumina adapters
		3′ adapter ligation 16 °C o/n in the presence of PEG
	TS5	HD adapters used instead of Illumina adapters
		3′ adapter ligation 16 °C o/n in the presence of PEG
		purification step after 3′ adapter ligation
	TS6	MRL adapters used instead of Illumina adapters
	TS7	MRL adapters used instead of Illumina adapters
		3′ adapter ligation 16 °C o/n in the presence of PEG
		purification step after 3′ adapter ligation
BIOO Scientific NEXTflex V2	Nf1	none: standard conditions
	Nf2	3′ adapter ligation 16 °C o/n
	Nf3	Illumina adapters instead of BIOO Scientific (HD) adapters
		3′ adapter ligation 16 °C o/n
	Nf4	no PEG in the ligation reactions
	Nf5	MRL adapters used instead of BIOO Scientific adapters
		no PEG in the ligation reactions
	Nf6	MRL adapters used instead of BIOO Scientific adapters
		3′ adapter ligation 16 °C o/n
New England Biolabs NEBNext	NN	none: standard conditions
Clontech SMARTer	S	none: standard conditions
Diagenode CATS kit	C	none: standard conditions

The Illumina TruSeq (‘TS’), BIOO Scientific NEXTflex V2 (‘Nf’) or Clontech SMARTer (‘S’) kits were used following their respective standard protocols or variants thereof. The different variants of the protocols are distinguished by numbers and their respective modifications are indicated