Table 1.

rRNA depletion methodologies for bacterial transcriptomics

Name	Catalog	Depletion strategy	Compatibility (fragmented RNA)	Cost per reaction	Notes
This work		RNase H degradation	Yes	∼$13	costs ∼$5 more for amplicon probes
Ribo-Zero™ rRNA Removal Kit (Bacteria)		Subtractive hybridization	Yes	∼$80	recently discontinued
MICROBExpress Bacterial mRNA Enrichment kit	ThermoFisher AM1905	Subtractive hybridization	No	∼$24	targets short conserved regions of rRNA
mRNA-ONLY Prokaryotic mRNA Isolation kit	Epicentre MOP51010	Exonuclease digestion	No	Inquiry required	based on 5′-monophosphate-dependent rRNA degradation
Trimmer-Direct cDNA Normalization Kit	Evrogen NK003	DSN-based normalization (24)	Yes	∼$33	potentially GC biased and low-efficiency (8)
Ovation Prokaryotic RNA-seq System	NuGEN 0326-32	Selective cDNA synthesis	No	∼$95	price includes reagents for library preparation
RiboMinus™ Transcriptome Isolation Kit, bacteria	ThermoFisher K155004	Subtractive hybridization	No	∼$48	targets short conserved regions of rRNA
Pan-Prokaryote riboPOOL	siTOOLs Biotech	Subtractive hybridization	No	∼$13	targets partial regions of rRNA