MAR 15, 2016 10:00 AM PDT

Gene Expression Analysis Using 3'-RNA Sequencing

Sponsored by: Lexogen, Lexogen
Speakers
  • Assistant Professor, University of Delaware
    Biography
      Behnam Abasht joined University of Delaware's faculty as an Assistant Professor in 2011. He received his PhD in Quantitative and Molecular Genetics in France from INRA-Agrocampus Rennes in 2006. He then completed a postdoctoral fellowship in Quantitative Genetics at Iowa State University. Dr. Abasht was a Research Geneticist and Genomics Project Leader at Perdue Farms, Inc. from 2008 until his appointment at the University of Delaware. His area of research is integrative avian biology with emphasis on fine-mapping and functional characterization of quantitative trait loci (QTL) in chickens.

    Abstract:
    10:00AM PT, 12:00PM CT, 1:00PM ET

    RNA sequencing (RNA-seq) has revolutionized the study of gene expression in animals, plants and microorganisms. However, because of its high cost, this technology has been mainly used in experiments with limited number of samples. To examine a cost-effective alternative, we used a method, which confines sequencing to the 3’-end of mRNA and produces just one fragment per transcript, resulting in a dramatic decrease in sequencing cost. Total RNA isolated from chicken adipose tissue samples was used for cDNA library preparation using QuantSeq 3’mRNA-seq library Prep Kit. Sixty-one uniquely indexed cDNA libraries were pooled and sequenced on one lane on the Illumina Hiseq 2500. On average, 2.24 million reads per sample were generated, 90.1% of which were mapped to the chicken reference genome (Ensembl Galgal4). For more than 70% of the genes with detectable expression, we redefined the 3’-end and identified alternative polyadenylation sites within the 3’-untranslated regions. To compare gene expression measures between 3’-RNA-seq and RNA-seq technologies, we used data from a subset of 20 samples that were previously used in a RNA-seq study of feed efficiency. The correlation of the log10(fold-change) for gene expression (high- vs. low-feed efficiency birds) between these two methods was 0.90. In conclusion, 3’-RNA-seq is a cost effective method amenable to global gene expression studies at population-level, e.g., expression QTL (eQTL) mapping.  Also, it allows for accurate detection of the 3’-end of transcripts, enabling verification of the current gene model annotations and global characterization of alternative polyadenylation.

    Learning objectives:

    1) Gain knowledge about 3’-RNA-seqencing and its application for global gene expression studies at population-level
     
    2) Explore how 3’-RNA-seqencing can help improve current gene model annotations and characterize alternative polyadenylation

     

    Show Resources
    You May Also Like
    SEP 05, 2019 4:00 PM CEST
    C.E. CREDITS
    SEP 05, 2019 4:00 PM CEST
    DATE: September 5, 2019TIME: 7:00am PT, 10:00am ET, 4:00pm CEST PCR (Polymerase Chain Reaction) has gone through a massive evolution since its development in 1983. Besides it...
    JAN 23, 2020 9:00 AM PST
    C.E. CREDITS
    JAN 23, 2020 9:00 AM PST
    DATE: January 23, 2020 TIME: 9:00am PST, 12:00pm EST...
    OCT 02, 2019 11:00 AM PDT
    OCT 02, 2019 11:00 AM PDT
    DATE: October 2, 2019TIME: 11:00am PDT, 2:00pm EDT Ditch the Excel spreadsheets and manage your molecular workflows entirely in your LIMS Achieve configuration of molecular workf...
    AUG 27, 2019 9:00 AM PDT
    C.E. CREDITS
    AUG 27, 2019 9:00 AM PDT
    DATE: August 27, 2019 TIME: 9:00am PDT, 12:00pm EDT Immunotherapies targeting PD-1 or PD-L1 have proven remarkably effective for treating cancer in some patients, with considerabl...
    FEB 26, 2020 9:00 AM PST
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    FEB 26, 2020 9:00 AM PST
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    DATE: February 26, 2020 TIME: 9:00am PST 3D cell culture and analysis and the study of organoids and spheroids are becoming more prevalent as a research method in publications as traditional...
    NOV 18, 2019 7:00 AM PST
    C.E. CREDITS
    NOV 18, 2019 7:00 AM PST
    DATE: November 18, 2019TIME: 7:00am PST, 11:00am EST, 4:00pm CEWT How often do you pipette in your cell culture lab every day? Usually, we do it so often that we tend stop th...
    Loading Comments...
    Show Resources