This hands-on two-part 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. For this first part of the workshop (wet lab), investigators must 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 (details are still being finalized), participants will receive instruction on how to analyze their own resulting sequencing data using computational and bioinformatics tools to obtain differential gene expression data.
This GSI-sponsored no cost two-part workshop is free and is 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 December 9, 2013.
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Part 1: RNA-seq Library Preparation
Date: January 9th and 10th, 2014
Place: BUMC Medical School Instructional Building, L401
Times: Thursday 1/9 – 9am-5pm and Friday 1/10 – 9am-4pm
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.
- 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).
- 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.
- Provide one experimental and one control high-quality total RNA sample (250-1000ng) to the BUMC Microarray Core Facility by the close of business on January 3, 2014. 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
Target Date: Late January/Early February 2014
Place: BUMC Medical School Instructional Building (TBD)
Time: Probably two 2-3 hour meetings
Goal: To acquire computational and bioinformatic analytical skills to generate differential gene expression results
The details of this workshop are still being determined.
- Generate differential gene expression results from your RNA-seq libraries prepared and sequenced in Workshop 1.
- Learn how to implement a computational analysis pipeline to move your sequencing data from raw reads to differential gene expression results.
Costs for cloud computing underwritten by the GSI