RNA-Seq Analysis Workshop


Unraveling the molecular mechanisms driving stem cell fate decisions still remains one of the major quests in stem cell biology. State-of-the-art -OMICS technologies have become an important tool to the discovery pipeline and have generated an increased interest among stem cell biologists in learning this technique. However, often technical and other practical challenges limit the ability of stem cell biologists to maximize the amount of information that can be harnessed from large data sets. Such limitations include 1) a lack of understanding of how next generation sequencing (NGS) works and how raw NGS data is acquired, processed and analyzed, 2) issues surrounding proper experimental design, 3) low number of stem cells available for genomic analysis, and 4) a limited understanding of the tools available for analyzing and interpreting obscure gene lists.

The Stem Cell Network and OIRM are pleased to offer the successful 2 to 3-day RNA-Seq Analysis workshop once again. Like last year, the single cell RNA-Seq analysis module has been expanded to address an increasing need. Day 3 of this workshop is by invitation, only for those trainees with their own RNA-Seq data, and will be spent on the analysis of these data beginning with alignments generated overnight of Day 2.

Who Should Attend?

This RNA-Seq Analysis workshop is designed for stem cell biologists (and other end users) who are looking to gain an appreciation of the bioinformatics concepts and processes used to acquire, analyze and interpret NGS data.

Workshop Learning Objectives

Through a mixture of interactive lectures and computer lab exercises, participants will be exposed to the RNA-seq data acquisition and analysis pipeline, and will gain hands-on training with available tools for network and pathway analysis of -OMICS data (focused on RNA-seq data, but applicable to data obtained from other platforms such as ChIP-seq, microarray or mass spectrometry). Workshop participants will also have the opportunity to ask questions and network with other stem cell biologists and bioinformaticists over the course of this workshop. Key objectives addressed in the course are:

  • Introduction to Next Generation Sequencing technologies and workflow, concentrating on RNA-seq.
  • Learn how to process raw NGS RNA-seq data into gene lists.
  • Gain an understanding of the different statistical tests used to analyze gene sets.
  • Hands-on training for determining functional enrichment of genes in a gene list using GSEA and gProfiler.
  • Hands-on training with network visualization tools including Cytoscape and Enrichment Maps.
  • Hands-on training with network and pathway analysis tools.
  • Learn how to perform single cell RNA-analysis through seminar and hands-on tutorials.

Workshop Dates:  October 16, 17 & 18, 2019
(Note that the sessions on October 18 have limited capacity and are only open to trainees with their own data sets ready for analysis. Attendance will be by invitation.)

Workshop Location: Roger-Guindon Hall, Room 2112, University of Ottawa, Ottawa, ON

Application DeadlineWednesday, August 28, 2019

Application Procedure & Registration Fees

Space in this workshop is limited; all those interested in participating must submit an application to attend the RNA-Seq Analysis workshop by Wednesday, August 28, 2019.

Selected applicants will be notified by Friday, September 6, and will be instructed on how to proceed with registration for the workshop.

The registration fees for the 2-day workshop are ($CAD):

  • OIRM trainees*: $450
  • Stem Cell Network trainees ‡: $450
  • Stem Cell Network or OIRM investigators: $500
  • Non-SCN and non-OIRM trainees or investigators: $700
  • Industry scientists: $1,000

The fee for participation in the tutorial Day 3 is an additional $225

* The definition of an OIRM trainee is a graduate student, post-doc, research associate and/or technician currently working in the lab of an OIRM principal investigator.

‡ The definition of a SCN trainee is a graduate student, post-doc, research associate and/or technician currently working in the field of stem cells and regenerative medicine in a Canadian lab.

Financial Support Available
The Ontario Institute for Regenerative Medicine (OIRM) and Stem Cell Network are offering a limited number of awards to enable eligible trainees to attend this workshop. All those who submit an application to attend will automatically be considered for trainee sponsorship and travel bursaries through the appropriate network.

Details of the OIRM / SCN Award and Application Procedure:
This OIRM / SCN award provides financial assistance for OIRM / SCN trainees to attend the RNA-Seq Analysis Workshop, October 16-18, 2019, organized by Dr. William Stanford, Dr. Ted Perkins, David Cook and Gareth Palidwor at the Ottawa Hospital Research Institute.


  • Application deadline is 11:59 PM (sender’s time) Wednesday, August 28, 2019.
  • The OIRM / SCN award will cover travel expenses associated with attending the workshop, for trainees not based in Ottawa (Travel to / from the workshop location, up to three nights shared accommodation at our designated hotel (the night before the workshop, day 1 and day 2, departure on day 3) and meals not provided during the workshop).
  • Reimbursement will be processed following the workshop and in accordance with the OIRM Travel Policy or the SCN Travel Booking & Reimbursement Policy (policies will be provided to the selected applicants).
  • Accommodation during the course will be provided for trainees not based in Ottawa. Two trainees of the same gender may be required to share a room.
  • Both the OIRM award and the SCN award will also cover the workshop registration fee (paid directly to the organizers).

Eligibility for the OIRM / SCN Award:

  • Applicants must be either an OIRM trainee (i.e. graduate student or post-doctoral fellow working in the lab of an OIRM principal investigator) or a SCN highly qualified personnel (i.e. a graduate student, post-doc, research associate and/or technician currently working in the field of stem cells and regenerative medicine in a Canadian lab.)
  • If you’re unsure whether you are an OIRM trainee, please consult the OIRM scientists list to see if your supervisor is part of OIRM or contact jodi.garner@oirm.ca.
  • If you’re unsure whether you are a SCN HQP, please email Rebecca Cadwalader at rcadwalader@stemcellnetwork.ca for confirmation.
  • Applicants must be working on a research project related to stem cells.
  • Applicants must clearly demonstrate that they will apply the techniques learned at the course to their own stem cell research project within one year.

Application Procedure:

  1. Complete the application form and return it, along with any additional documents required, by email to rcadwalader@stemcellnetwork.ca by 11:59 PM (sender’s time) Wednesday, August 28, 2019.
  2. The OIRM /SCN Training & Education Committees will review all complete applications, and applicants will be informed of the competition outcome by Friday, September 6, 2019.

Workshop Requirements:
Note that participants in this workshop are required to use their own laptop computers, and the laptop must be able to run Oracle Java 7. Please ensure that your laptop is able to run Oracle Java 7 before applying to for the OIRM / SCN travel award. Participants will also need to download free software tools before attending the workshop, and will be advised of what software is required following their registration in the workshop.

Reporting and Communication Requirements:
By accepting an OIRM / SCN award, the recipient agrees to provide a report describing the value of the training and networking opportunities made available through the award. This information will be used at OIRM’s / SCN’s discretion on its website, newsletters and for the purpose of reporting to their funding agencies. By registering for this workshop attendees also accept to have their pictures taken during workshop and used in reporting tools as mentioned above. Please note that expense reimbursement will be processed only once the completed report is received.

For further information on this workshop or for application related enquiries please contact Rebecca Cadwalader at rcadwalader@stemcellnetwork.ca

Other Workshops