Illumina Next Generation Sequencing Facility

Next generation sequencing (NGS) has rapidly become the state of the art for high-throughput genomic analyses. This robust technology provides access to numerous applications ranging from genomic (re)sequencing, whole-transcriptome analysis, small RNA, miRNA, non-coding RNA, targeted sequencing, ChIP-Seq and ATAC-Seq. Using a massively parallel sequencing approach, NGS is capable of generating gigabases of high quality sequence, maximizing throughput while minimizing the cost and time to generate this data. Infrastructure funding for this facility has been provided through a partnership with The Ottawa Hospital to provide research capacity to the Eastern Ontario Regional Laboratory Association (EORLA) personalized medicine initiative and by the Canadian Foundation for Innovation.

StemCore's Next Generation Sequencing Facility is equipped with Illumina's NextSeq 500 and MiniSeq. Our facility also has access to the new NextSeq 2000 located at the University of Ottawa Centre for Advanced Research in Environmental Genomics (CAREG). The NextSeq 2000 employs the proven sequencing by synthesis (SBS) technology, and innovative patterned flow cell technology which delivers significant increases in sequencing reads and total output.

With these instruments StemCore can provide access to a wide variety of scalable next generation sequencing (NGS) applications with data ranging from 7.5 Gb up to 360 Gb generated per sequencing run. These platforms deliver high quality data with reduced cycle and data processing times and allow greater flexibility in experimental design and faster turn-around-times for small to large scale projects.

• Nucleic Acid Quality Assessment and Quantitation
• Library Construction
• Library Sequencing
  • StemCore or User Prepared
• Consultation
  • Experimental Design
  • Pilot Projects
  • Proof of Concept Experiments
  • Grant Support
  • Manuscript Preparation
  • We will provide all support necessary to bring your project to successful completion.
  • Please contact Damian Carragher to discuss

• A Master Service Agreement must be established and signed by the PI and Institutional Signing Authority (external clients) for each project prior to processing samples. The agreement will be in effect for three years from the time of signing.
• All NGS service requests must be entered and approved in UOttawa Infinity Idea Elan prior to sample submission
• Samples should be accurately quantitated using a fluorometric method (PicoGreen, RiboGreen, or Qubit). StemCore Laboratories is able to perform these assays for a nominal fee. NanoDrop readings are not accurate at the very dilute concentrations utilized in next generation sequencing protocols, especially for ChIP-Seq applications.
• StemCore is experienced in a wide variety of library preparation protocols. If your application is not listed below please contact us to discuss.
• Input samples and NGS libraries will be stored for a limited period after which the PI will be notified to retrieve the samples if desired, otherwise samples will be discarded.
• Please contact StemCore for library preparation and sequencing pricing.

In most cases, BaseSpace will be utilized to facilitate transfer ownership of data. When sequencing is complete, you will be provided a link to facilitate this transfer. More information regarding BaseSpace and data transfer can be found here: https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000002876

In cases where data transfer cannot occur within BaseSpace, you will be provided directions to obtain your data electronically.

StemCore will not archive analysis files once the data has been provided.

A wealth of information regarding next generation sequencing is available on the internet. While this list is by no means meant to be exhaustive it provides links to some helpful sites for next generation sequencing applications, protocols, guidelines, and analysis tools:

• Illumina
• BaseSpace
• SeqAnswers
• AllSeq
• Biostars
• MACS (Model-based Analysis for ChIP-Seq)
• ENCODE and ENCODE Data Standards and Guidelines

Ottawa Hospital Research Institute
Sprott Center for Stem Cell Research
StemCore Laboratories
Room 5132, Critical Care Wing
501 Smyth Road
Ottawa, Ontario, Canada K1H 8L6

Caroline Vergette
cvergette@ohri.ca
613.737.8899 x73251 (lab phone)
613.739.6294 (fax)

Damian Carragher
dcarragher@ohri.ca
613.737.8899 x73110 (office)