Workshop Description

This workshop aims to provide the basics tools to navigate into RNA-seq data analyses. This workshop will be divided into three major sections of two days each covering different steps of RNA-Seq analysis: 1) read alignments; 2) differential gene expression analysis; 3) gene set enrichment analysis and visualization of results. These sections will cover typical workflow of RNA-Seq study from raw reads to final results. Each section will represent independent step of RNA-Seq data analysis based on the same case study. You can register to the whole workshop or separately to any particular section.

To access the workshop slides, click here.

Section 1: Intro to RNA-Seq

From reads to alignments (taught by Trent Su, Ph.D):

  • Concept of RNAseq and experimental design
  • Quality checking of RNAseq reads
  • Mapping reads to genome
  • Visualization of mapped reads with IGV and IGB

Section 2: Analysis with R, gene expression

From alignments to differentially expressed genes (taught by Alice Mouton Ph.D):

  • Gene counts
  • Normalization of gene counts
  • Differential Gene Expression analysis
  • Adjusting for multiple tests

Section 3: Analysis with R, functional analysis

From differentially expressed genes to biology (taught by Yerbol Kurmangaliyev):

  • Visualization of gene expression analysis
  • Gene set and pathway enrichment analysis

Workshop Materials

  • For Section 1 and 2: Attendees are required to have a Hoffman2 account. To obtain an account, click here.
  • For Section 2 and 3: Attendees are required to have pre-installed R and Rstudio
  • Other details will be sent to registered attendees by email prior to workshop.

Instructor

Trent Su is a postdoctoral fellow at Dr. Siavash Kurdistani lab in the Department of Biological Chemistry. In collaboration with Dr. Arnie Berk lab, his research focus on using high-throughput genomics methods to study genome-wide epigenetic changes induced by Adenoviral oncoprotein e1a which upon expression forces stationary host cells into S phase. Dr. Su received his B.S. in Molecular and Cell Biology at UC Berkeley. Afterwards, he received his M.S. in Computer Science at UC Irvine where he co-written a java web application for Systems Biology pathway modeling. He completed his PhD training in the Kurdistani lab and received his PhD in Oral Biology at UCLA School of Dentistry. His current interests include writing custom python scripts for high-throughput sequencing analysis and mining cancer mutation databases.

Email: ytsu@ucla.edu

Dr. Alice Mouton is an Assistant Project Scientist in Robert Wayne laboratory in the department of Ecology and Evolutionary Biology. Her current researches focus on applying gene expression methodologies (RNA-seq and RRBS) to study non model organisms (bobcat, island fox) in a context of conservation.

Dr. Yerbol Kurmangaliev is currently a postdoctoral researcher in the laboratory of Professor S. Lawrence Zipursky. He earned a M.S. degree in Biochemistry at Lomonosov Moscow State University in 2006. He earned a Ph.D. degree in Bioinformatics at Kharkevich Institute for information transmission problems of the Russian Academy of Sciences in 2011 under the supervision of Professor Mikhail S. Gelfand. Before joining to UCLA he was a postdoctoral researcher in the laboratory of Professor Sergey V. Nuzhdin at USC. His previous research interests have been primarily focused on genetic basis of gene expression.

Workshop Details

Prerequisites: W1, W2
Recommended: W3
Length: 6 days, 2hrs per day
Level: Introductory, intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Spring Dates

Sec. 1: 4/25/17 – 4/26/17, 1PM
Sec. 2: 5/15/17 – 5/16/17, 1PM
Sec. 3: 5/17/17 – 5/18/17, 1PM