2015 RNA-seq data generation and analysis hands-on workshops

This hands-on workshop is designed to offer BU researchers the opportunity to generate mRNA-seq differential expression data that can be used as preliminary data for extramural grant applications.  The workshop will be compose of two parts: data generation and data analysis.  For the first part of the workshop (wet lab), investigators will supply their own experimental and control RNA samples and will be trained in sample preparation methods to generate directional RNA-seq libraries.  These libraries will then be high throughput (deep) sequenced using the Illumina HiSeq platform.  In the second part of the workshop, participants will learn how to analyze the resulting NGS sequencing data using computational and bioinformatics tools to obtain differential gene expression data.

This GSI-sponsored no cost workshop is free and open to all researchers at BU.  Because there is a 24 participant limit, we may request additional information in order to select participants.  The deadline for application is April 7, 2015.

Please register here

For more details please email gsi@bu.edu

Part 1: RNA-seq Library Preparation

Dates: May 6-7, 2015

Place: BUMC Medical School Instructional Building, L401

Time: 9 a.m.-5 p.m. daily

Goal: Generate high throughput sequencing libraries from participant-provided total RNA samples

  • A two day hands-on wet lab workshop, taught by experts from NEB and BU.
  • Participants will prepare directional mRNA-seq libraries using NEBNext Ultra Directional RNA Library Prep Kits for Illumina and their own experimental and control samples (one of each).
  • We will utilize the NEBNext rRNA Depletion Kit (Human/Mouse/Rat), so libraries can only be prepared using RNA from these three species.
  • Libraries will be sequenced on the Illumina HiSeq platform using a multiplexing strategy.  Single end 50bp reads will be generated with a target of 20-25 million reads/sample.

Participant Responsibilities:

  • Provide one experimental and one control high-quality total RNA sample (500-1000ng) to the BUMC Microarray Core Facility by the close of business on April 27, 2015.  Each RNA sample will be quantitated and assessed for quality using an Agilent Bioanalyzer.
  • You will be asked to bring some basic lab supplies to the workshop (e.g., pipettes, pipet tips, an ice bucket, etc.).

    Generously Sponsored by New England Biolabs
    Costs for high throughput sequencing underwritten by the GSI

    Part 2: Computational Analysis of High Throughput RNA-seq Data

    Date: TBA

    Place: TBA

    Time: TBA

    Goal: Learn how to implement a computational analysis pipeline to move your sequencing data from raw reads to differential gene expression results.

    Participants will learn how to process and initially analyze the generated data using the GSI-sponsored Globus Genomics Galaxy Platform (http://www.bumc.bu.edu/gsi/initiatives/globus-genomics/) to obtain differential gene expression data.

    Developed in collaboration with Globus Genomics