Chat #5: rRNA removal and optimization of host-bacterial expression data

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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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Cataloging the identity and metabolic profiles of gut microbes is an emerging application with high-impact in health and disease management.  While efforts have been made to catalog the presence of microbes, future work will focus on how microbes are functioning at both the species and community levels and how host cells are responding to these changes. RNAseq has emerged as the best method to profile the interplay between the microbes and their hosts.

One challenge to using RNAseq is the low levels of biologically relevant RNA in a background of ribosomal RNA.  QIAGEN has developed the QIAseq FastSelect HMR and QIAseq FastSelect 5S/16S/23S rRNA removal reagents to give researchers the ability to perform microbe and host gene expression profiling from human, mouse, rat and other mammalian samples.  FastSelect 5S/16S/23S was designed 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 >95% of all 5S, 16S and 23 rRNA databased sequences.

Join QIAGEN’s RNAseq R&D team for a discussion on how we developed and benchmarked QIAseq QIAseq FastSelect 5S/16S/23S and QIAseq FastSelect HMR for profiling gene expression of microbes and host cells, followed by Q&A with the experts.

Jonathan Shaffer, Ph.D.

Jonathan M. Shaffer
Dr. Shaffer joined QIAGEN in 2009 and has since worked with various technology development groups, the most recent being miRNA technologies. He received his Ph.D. in biochemistry and molecular genetics from the University of Pittsburgh School of Medicine in 2008 where his research focused on determining the mechanisms that regulate non-receptor tyrosine kinase expression and activity. Dr. Shaffer did his postdoctoral training at SABiosciences Corporation, now part of QIAGEN. Currently, Dr. Shaffer is a Senior Scientist in Product Development at QIAGEN.