Table 1.

Displayed are the different steps (columns) in gene expression analysis

	RNA extraction	cDNA synthesis	Preamplification	qRT-PCR
Conventional workflow
Kits used	mirVana miRNA Isolation Kit	High-capacity cDNA reverse transcription kit		TaqMan Universal PCR Master Mix
Task	Extraction of total RNA	cDNA synthesis using random primers		qRT-PCR specific for the concerning targets
Modified workflow
Kits used	Oragene protocol  + mirVana miRNA Isolation Kit	SuperScript III First-Strand Synthesis SuperMix Kit	Taqman PreAmp Master Mix Kit	TaqMan Universal PCR Master Mix
Task	Extraction of total RNA from whole saliva (human – panbacterial)	cDNA synthesis from human RNA by using oligo(dT) primers	Unbiased and multiplex amplification of up to 100 targets	Unbiased qRT-PCR specific for the concering targets
Rationale	Isolation of RNA from whole saliva	poly(A) + -selected human cDNA	Increase quantity of human cDNA	Unbiased qRT-PCR

Also shown are the comparisons between the conventional workflow (suggested by the manufacturer) and our modified workflow, including the required kits, the tasks and the rationale for our modifications.