Chat #4: Overcoming challenges of rRNA removal with complex bacterial samples for RNA-seq

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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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Metagenomic and transcriptomic analysis from complex bacterial samples is gaining popularity due to the ease of obtaining samples and the decreased costs of next generation sequencing.  While DNA profiling using 16S profile or even shot-gun genomic sequencing has become routine, RNA profiling presents a special challenge due to prokaryotic 5S/16S/23S rRNA contamination and its removal that is essential for obtaining relevant gene expression data.  

For complex bacterial samples, continued evolution of our first generation QIAseq FastSelect technology recently resulted in a new strategy that is extremely efficient in removing 5S/16S/23S rRNA.  We designed QIAseq FastSelect -rRNA Removal 5S-16S-23S 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 block greater than 95% of all 5S, 16S and 23 rRNA databased sequences. Use of the QIAseq FastSelect -rRNA Removal 5S-16S-23S Kit with our latest mammalian QIAseq FastSelect -rRNA Removal HMR kit allows researchers to address complex samples from humans, mouse, rats and other mammalian samples without changing their workflow.

Join QIAGEN’s RNA-seq 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 from complex samples sources, followed by Q&A with the 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.