SCN ATAC-seq Workshop

Application Deadline: July 10, 2023
Workshop Date: September 8, 2023
Time: 11 a.m. – 5 p.m. ET
Location: Online (link to be provided)

ATAC-seq is an advanced bioinformatics technique that is used to determine chromatin accessibility and increase understanding of how chromatin packaging influences gene expression. The SCN ATAC-seq workshop is a practical introduction to bulk and single-cell ATAC-seq data analysis presented by Dr. Theodore Perkins, Dr. David Cook and the Ottawa Bioinformatics Core Facility.

Who Should Attend?
Trainees and researchers who want to better understand ATAC-seq experimental and analysis methodology and those who wish to analyze their own data or re-analyze published ATAC-seq data. Recent completion of the SCN RNA-seq analysis workshop is a prerequisite to participate in this workshop (within the last three years).

Workshop Learning Objectives:

This workshop will provide:

  • A basic understanding of bulk and single cell ATAC-seq technologies and experimental design.
  • Experience with bulk and single cell analysis pipelines that covers ATAC-seq analysis starting from an ATAC-Seq Count Matrix, including:
    • Data importation, cleaning and quality review
    • Normalization
    • Visualization
    • Annotation by genomic position
    • Differential chromatin accessibility
    • Motif enrichment in peaks

 This workshop will be delivered by the Ottawa Bioinformatics Core Facility with speakers including: Dr. Theodore Perkins, Dr. David Cook, Gareth Palidwor, and Christopher Porter.

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Dates & Location

Dates: September 8, 2023
Time: 11 a.m. – 5 p.m. ET
Location: Online

How to Apply

  • Complete the application form by 12 PM ET, July 10, 2023.
  • The SCN Training & Education Committee will review all complete applications, and applicants will be informed of the competition outcome by late July. Notification of acceptance for successful applicants will include a registration link for joining the online workshop sessions.
  • Provide a full letter of support from your current supervisor detailing how your attendance will benefit your research and the lab’s stem cell research program as a whole. Letters should be e-mailed by supervisors directly to Ellie Arnold, earnold@stemcellnetwork.ca at the same time you submit your application documents. A confirmation email will be sent within 24 hours of SCN receiving the submitted support letter. If a confirmation email is NOT received from SCN within 24 hours of submission, it is the responsibility of the applicant to contact SCN and ensure that all application materials have been received by SCN.


  • Applicants must be a trainee/highly qualified personnel (HQP) (i.e., a graduate student, post-doc, research associate and/or technician currently working on a research project in the field of stem cells and regenerative medicine in a Canadian lab.)
  • Non-academic applicants are welcome to apply, however academic applicants are prioritized. A $700 registration fee will apply to all non-academic participants.
  • If you’re unsure whether you are a trainee/HQP, please email Ellie Arnold at earnold@stemcellnetwork.ca for confirmation.
  • Applicants must clearly demonstrate that they will apply the techniques learned at the course to their own stem cell research project within one year.


  • Participants must have a computer with a microphone (and optionally a camera) and a high-speed internet connection. 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. A second monitor or screen will be required to enable participants to simultaneously use the software tools and view the workshop video stream.
  • Spaces are limited for this training opportunity. SCN will cover the registration costs (paid directly to the organizers) of this workshop for applicants who attend all sessions and complete all elements of the online content within the designated period. For applicants who fail to attend all sessions or complete the course content, a fee of $700 will be charged to their supervisor to cover the costs associated with delivering this training opportunity. Applicants should ensure their PI is aware of this condition at the point of application.
  • By accepting a place on this workshop, the recipient agrees to complete a survey describing the value of the training and networking opportunities made available through the award. This information will be used at 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 the workshop and used in materials as described above.

For further information on this workshop or for application-related enquiries, please contact Ellie Arnold at earnold@stemcellnetwork.ca.

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