Yorba Linda, CA (PRWEB) February 23, 2016
The study of gene expression in animals, plants, and microorganisms has been fundamentally transformed by the use of RNA sequencing (RNA-seq). This technology has chiefly been used in experiments with a limited number of samples due to its steep cost. In pursuit of a less costly option, an alternate method was used, one that confines sequencing to the 3’-end of mRNA and produces only one fragment per transcript. This approach sharply lowered the sequencing cost.
Researchers used total RNA isolated from chicken adipose tissue samples for cDNA library preparation with the QuantSeq 3’mRNA-seq library Prep Kit from Lexogen. In this process, 61 uniquely indexed cDNA libraries were pooled and sequenced on one lane on the Hiseq 2500 ultra-high-throughput sequencing system from Illumina. Typically, 2.24 million reads per sample were produced, with about 90% mapped to the chicken reference genome. The researchers redefined the 3’-end and found other polyadenylation sites within the 3’-untranslated regions for upwards of 70% of the genes with detectable expression.
They applied data from a subset of 20 samples that had been used earlier in a RNA-seq study of feed efficiency to compare gene expression measures between 3’-RNA-seq and RNA-seq technologies. The correlation of the log10 (fold-change) for gene expression (high- versus low-feed-efficiency birds) among these methods was 0.90. The researchers determined that 3’-RNA-seq is a cost-saving method applicable to global gene expression studies at population-level such as expression QTL (eQTL) mapping—and, it permits accurate detection of the 3’-end of transcripts, thus enabling verification of the current gene model annotations and global characterization of alternative polyadenylation.
Lexogen is sponsoring a new, free educational webinar, “Gene Expression Analysis Using 3’-RNA Sequencing,” which will discuss the researchers’ methods and approaches.
The speaker is Behnam Abasht, PhD, assistant professor at the University of Delaware. Dr. Abasht received his PhD in quantitative and molecular genetics from INRA-Agrocampus, Rennes, France. He completed a postdoctoral fellowship in quantitative genetics at Iowa State University, and was a research geneticist and genomics project leader at Perdue Farms prior to his appointment at the University of Delaware. Dr. Abasht’s area of research is integrative avian biology with emphasis on fine-mapping and functional characterization of quantitative trait loci (QTL) in chickens.
The free webinar, hosted by LabRoots, will be presented on March 15, 2016, at 10 am PT/12 pm CT/1 pm ET.
For full details about the event and free registration, click here.
Lexogen, Vienna, Austria, is a biotech company that offers proprietary expression profiling technologies that enable detailed analysis of the complete transcriptome and individual full-length RNAs of interest. The company was founded in 2007 with the support of private capital and public funds, and is supported by the Austrian Research Promotion Agency FFG, the Austria Wirtschaftsservice AWS, INiTS, and the Wirtschaftsagentur Wien. Half of its employees work in research and development. The company has a US subsidiary based in New Hampshire.
LabRoots is the leading scientific social networking website and producer of educational virtual events and webinars. Contributing to the advancement of science through content sharing capabilities, LabRoots is a powerful advocate in amplifying global networks and communities. Founded in 2008, LabRoots emphasizes digital innovation in scientific collaboration and learning, and is a primary source for current scientific news, webinars, virtual conferences, and more. LabRoots has grown into the world’s largest series of virtual events within the Life Sciences and Clinical Diagnostics community.