Single-cell sequencing

Date 12 - 13 October 2016
Speaker(s) Brian Haas, Timothy Tickle
ECTS 0.5
Fees *academic: 100 CHF   -   for-profit: 0 CHF
Cancellation deadline 7 Oct 2016
City Bern
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


Single cell transcriptome studies are transforming our knowledge about cell types and cell states, and revealing important variation in gene expression that is otherwise hidden in the context of bulk measurements. Single cell RNA-Seq technology and analysis tools are rapidly evolving, and the complexity of such studies necessitates careful statistical considerations. In this workshop, we provide an overview of the sequencing technologies and experimental methods that make possible single cell transcriptome sequencing. Through hands-on activities with single cell RNA-Seq data, we explore analysis methods available for exploring the variation in transcript expression among cells, define clusters of related cells, and identify characteristics of cell types that are relevant to their biological function.

Invited lecturers:

  • Brian Haas, Broad Institute, Cambrigde, USA
  • Tim Tickle, Broad Institute, Cambrigde, USA

Learning objectives

The overall theme of this course will center on how single-cell RNA-Seq is different than population based RNA-Seq and, due to those differences, how analysis methodology differs. Participants will have an understanding of how sequence data is generated using the most common single-cell RNA-Seq assays. Participants will form an intuition on how single-cell RNA-Seq expression data is different and how that affects the selection of methodology for analysis. Participants will use popular R libraries to perform quality control, plotting, and analysis targeting both cell heterogeneity and genes that may discriminate those groups.

Bring your own data (optional attendance):

Friday 14th of October is a great opportunity for the participants of the "Single Cell sequencing" and "De novo Transcriptome assembly" workshops to bring their own data and start their analysis onsite and/or ask questions concerning their own research expermiental design.

Location: Room 331 3.OG/West, University of Bern, Hochschulstrasse 4, Bern, Switzerland (MAP)

Registration for this day is free of charge but mandatory, the first 30 registrations will be accepted for attendance (room space allowance):

Bring your own data registration here.


Knowledge / competencies:

Attendees should already be familiar with the basic terms and concepts of genetics and genomics.


Attendees should bring their own laptop computers.

For the practical tutorial, basic familiarity with the command line environment is required. Basic knowledge in R-statistics is recommended but not mandatory.

Prior to the course, please download the Integrative Genome Viewer (IGV).

Schedule overview

Morning: Overview of laboratory prep and sequence analysis
Afternoon: Characteristics of expression data and QC

Morning: Plotting Single Cell RNA-Seq data
Afternoon: Evaluating and defining cell populations


University of Bern, Switzerland

Wednesday 12th October:
Hochschulstrasse 4, Room 331 3.OG/West (MAP)

Thursday 13th October:
Schanzeneckstrasse 1, Room A301/ UniS (MAP)

Additional information

Organizer: Walid Gharib, Training Group – Swiss Institute of Bioinformatics & IBU - Interfaculty Bioinformatics Unit - University of Bern

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