Table 2. Methods used for preparing and sequencing samples through two independent NGS runs.

Site	NGS round	Extraction kit (Qiagen)	Reverse transcription approach*	Product clean-up**	Library type	# of indexing PCR cycles	Illumina platform
Blue	1	QIAamp MinElute Virus Spin kit	Random hexamers	AMpure XP beads	cDNA	20	NextSeq
	2	RNeasy kit	Random hexamers	Spin Column	cDNA	18	HiSeq
	2	RNeasy kit	SISPA	Spin Column	SISPA	5	HiSeq
Ichetucknee	1	QIAamp MinElute Virus Spin kit	Random hexamers	AMpure XP beads	cDNA	20	NextSeq
	2	RNeasy kit	Random hexamers	Spin Column	cDNA	18	HiSeq
	2	RNeasy kit	SISPA	Spin Column	SISPA	5	HiSeq
Manatee	1	QIAamp MinElute Virus Spin kit	Random hexamers	AMpure XP beads	cDNA	20	NextSeq
	2	RNeasy kit	Random hexamers	Spin Column	cDNA	18	HiSeq
	2	RNeasy kit	SISPA	Spin Column	SISPA	5	HiSeq
Rainbow	1	QIAamp MinElute Virus Spin kit	Random hexamers	AMpure XP beads	cDNA	20	NextSeq

Notes:

^*Distinguishes if cDNA was obtained using random hexamers included with the Superscript First-Strand Synthesis System (Invitrogen) or primers used for sequence-independent, single-primer amplification (SISPA).

^**Procedure used to clean-up Klenow reaction products (cDNA libraries) and SISPA products prior to NGS library preparation. The spin column procedure was performed with the DNA Clean & Concentrator®-25 kit (Zymo Research).