biostudies-literatureWahl ATechnische Universität MünchenDeutsche Forschungsgemeinschaft5765https://www.ebi.ac.uk/biostudies/studies/S-EPMC8986838biostudies-literatureUnknown12(1)Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA dScientific reportsComparison of rRNA depletion methods for efficient bacterial mRNA sequencing.PMC89868381401/1-1Wahl AHuptas CNeuhaus KfalseComparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA d2022-01-01T00:00:00Z2022 Apr2026-05-30T20:57:44.669Z2025-04-04T10:02:24.489ZS-EPMC89868383538807810.1038/s41598-022-09710-y