RNA-Seq Workshop: Library Preparation and Introduction to Data Analysis

May 10, 2016, 9 a.m. - May 12, 2016, 6 p.m.

Organizer -

DNA Technologies Core

Contact -

UC Davis Bioinformatics Core, bioinformatics.core@ucdavis.edu

RNA-seq has revolutionized the way we address complex biological questions, allowing for differential gene expression, differential transcript analysis, as well as transcriptome assemblies. As sequencing output rapidly increases and sample numbers increase, library preparation becomes one of the major bottlenecks. This workshop provides comprehensive hands-on training in the preparation of high quality RNA-Seq libraries for the Illumina platform. Participants will generate two types of RNA-seq libraries: one using poly-A enrichment and one using ribo-depletion. The former protocol is preferred for high quality eukaryotic RNA samples.  The latter is required for bacterial RNA-seq and fragmented RNA samples.  Lectures will cover the entire workflow including sample QC/QA, as well as the basic principles of Illumina technology and considerations for experimental design meeting current publication standards.  Approximately 6 hours will be spent on data analysis, presented by the Bioinformatics Core, and will include an introduction-to/demo-of RNA-seq data QA/QC, preprocessing, read mapping, gene counting as well as a hands-on-exercise on Differential Expression Analysis in R with previously computed gene counts tables.

The hands-on data analysis portion will comprise approximately 2 hours of this workshop. For more in-depth instruction on bioinformatic analysis of RNA-Seq (and other types of high throughput sequencing) data, you may wish to attend the June Bioinformatics Workshop, Using Galaxy for Analysis of RNA-Seq and ChIP-Seq Data (https://registration.genomecenter.ucdavis.edu/).

Registration is limited to 12 participants due to lab space constraints. RNA samples will be provided. The workshop will conclude with an evaluation of library quality and a discussion session focusing on each participant’s experimental design to help maximize efficiency and output of sequencing experiments.

Participants are required to bring a set of adjustable volume micro-pipettes to the workshop as well as a laptop computer (Windows, Mac, Linux) for the data analysis part.

Registration fees are $400 for UC participants, $500 for other academic/non-profit participants and $600 for industry/for-profit.

The workshop will be held on the UC Davis campus and will run from 9am to 6pm each day. Lunches will be provided.  

Questions? Contact Lutz Froenicke (lfroenicke@ucdavis.edu) for wet-lab and training.bioinformatics@ucdavis.edu for data analysis questions.

This workshop is a joint production of the DNA Technologies and Expression Analysis Cores and the Bioinformatics Core.

Registration is closed for this event