Chat #2: Increasing bacterial RNA-seq sensitivity through efficient rRNA removal

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Learn more about QIAseq FastSelect –rRNA HMR Kits

Learn more about QIAseq FastSelect –5S/16S/23S Kits

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Exploring gene expression among prokaryotic samples and communities involves using RNAseq methods to identify and quantify the gene expression components.  Prokaryotic RNA profiling presents a special challenge for RNAseq analysis because (1) removal of prokaryotic 5S-16S-23S rRNA is necessary to achieve adequate sensitivity for detection of low level gene expression and (2) the diversity in rRNA sequencing challenges even the best methods for complete rRNA Removal.

Evolution of QIAGEN’s QIAseq FastSelect rRNA removal technology has recently resulted in the design of an extremely robust system for 5S-16S-23S rRNA removal.  We designed it to block community level cDNA synthesis of 5S,16S and 23S rRNA against SILVA 16S sequences (nearly 600,000 entries), SILVA 23S sequences (nearly 170,000 entries) and 5S rRNA Database (over 7,200 entries) and theoretically blocks greater than 95% of all 5S, 16S and 23 rRNA databased sequences. Moreover, the process only involves a simple 14-minute incubation with the FastSelect 5S-16S-23S reagent plus standard bead cleanup. This novel chemistry allows researchers to achieve high levels of rRNA removal from complex bacterial samples such as soil, water and stool. 

Join QIAGEN’s RNAseq R&D team for a discussion on how we developed and benchmarked QIAseq QIAseq FastSelect 5S-16S-23S using both high quality and severely fragmented RNA samples, followed by Q&A with our experts.

Dr. Sam Rulli

Samuel J. Rulli

Samuel Rulli is an R&D Scientist in qPCR applications at QIAGEN and has spent three years in the biotech industry as a qPCR specialist developing, evaluating, and teaching different qPCR technologies and applications. Dr. Rulli received his PhD in 2002 from Tulane University studying the gastric proton pump and did post-doctoral research at Johns Hopkins University and the National Cancer Institute in Frederick, MD. Trained as a molecular biologist, Dr. Rulli has worked on different assay detection technologies for gene expression and nucleic acid analysis.