Table 6.

Number of transcripts declared differentially expressed (DE) using DESeq2

	All transcripts			High-count transcripts	Low-count transcripts
	Total	SB-only	BB-only	Total	Total	SB-only	BB-only
No filter	2290	112	69	38	1325	112	69
RP filtering	2297	111	69	38	1327	111	69
CPM filtering	952	0	0	30	204	0	0

The table contains the number of total transcripts, high-count transcripts and low-count transcripts declared DE using DESeq2 analyses on the complete dataset (i.e. no data filtering applied) or following data filtering based on reads-present (RP) criterion or counts per million (CPM) criterion. Also listed are transcripts with expression levels present in sand bluestem and absent in big bluestem (SB-only transcripts) and transcripts with expression levels present in big bluestem and absent in sand bluestem (BB-only transcripts)