How can you use Rubicon Genomics’ Technology in your research?

 

Egon Ranghini, PhD, Applications Scientist on December 30, 2016

The technology behind Rubicon Genomics’ NGS library preparation kits is used to produce high quality Illumina® NGS libraries using a simple, single tube, three step workflow. Publications in top journals were released this year showing how our technology can be used in a variety of applications including ChIP-seq, RNA-seq, FFPE, single cell sequencing, CNV detection and more. Recently, a paper published in BMC Plant Biology used our ThruPLEX® DNA-seq library preparation kit to reveal the effects of cytokinin on gene expression in shoots and roots of O. sativa (rice) by using NGS-based whole transcriptome analysis. To analyze gene expression in response to the cytokinin benzyladenine (BA) in roots and shoots, ThruPLEX DNA-seq was used to generate sequencing-ready libraries from cDNA prepared from rice seedling treated with BA. After sequencing, it was discovered that more than 95% of reads mapped to a single location in the rice genome. Many of the 30,000 genes identified were expressed in both tissues. In the control, more than 17,000 genes were differentially expressed between roots and shoots compared to BA treatment, where approximately 4,700 genes and 2,400 genes were differentially expressed in roots and shoots, respectively. A subset of differentially expressed genes was chosen to confirm the RNA-seq analysis by using the NanoString nCounter assays. RNA-seq results were confirmed for the vast majority of the genes re-tested, thus indicating high confidence in the RNA-seq analysis. Gene ontology (GO) analysis revealed that transcription factors, receptor-like kinases, genes involved in protein degradation and genes controlling development in response to biotic stress were regulated by cytokinin in rice. Interestingly, this study unveiled a substantial overlap between genes differentially expressed upon cytokinin treatment and those regulated by various pathogens, hence suggesting that cytokinin may play a crucial role in the transcriptional response to biotic stress in rice.

For more information about this article or to learn how Rubicon Genomics’ library preparation kits can be used in other applications, download our publication list!