Workshop Description

This workshop aims to provide an entry-level introduction to the basic concepts and data analysis tools for single-cell RNA-seq techniques. It will help the attenders obtain a better idea of the important applications of scRNA-seq, the important considerations in designing a scRNA-seq experiment, the major differences between popular technical platforms, and the main steps in preliminary data analysis. It can serve as a starting point to conceive a scRNA-seq study or to analyze a scRNA-seq dataset.

Day 1

Session 1 (Emily Wu): Intro to scRNA-seq basics

  • Concept of scRNA-seq and main applications
  • Important issues in experimental design
  • Comparison between popular technical platforms
  • Raw data processing

Day 2

Session 2 (Yerbol Kurmangaliyev): Guided case study using Seurat;

  • Overview of scRNA-Seq analysis and logistics of Seurat;
  • Data preprocessing: loading, QC/filtering, normalization/scaling;
  • Dimensionality reduction and clustering;
  • Identification of marker genes;
  • Visualizations.

Workshop Materials

The first 10 attendees can use the classroom computer, others can attend if using their own laptop. The room is equipped with ethernet jacks and wireless internet.


Dr. Emily Wu is currently an assistant project scientist in the laboratory of Dr. Weizhe Hong in the Department of Biological Chemistry. Her current research interest focuses on applying and developing single-cell RNA sequencing methods and circuit manipulation for the molecular and functional dissection of neural circuitry underlying animal behaviors. She received her B.S. in Biology from Peking University, China. She then earned her Ph.D. from Stanford University where her graduate research focused on molecular and cellular mechanisms governing synapse formation and axonal transport in neurons. Afterwards, she worked as a postdoctoral fellow in Dr. Daniel Geschwind’s lab at UCLA where she investigated the neural mechanisms of autism spectrum disorders through functional genomic and animal behavioral studies.

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: Basic experience with R would be helpful but not required
Length: 2 days, 2 hours
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Fall 2018 Dates

October 30 and 31, 2018
1:00 PM – 3:00 PM