Illumina Next Generation Sequencing Facility
Overview
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.
Facility
StemCore's Next Generation Sequencing Facility is equipped with Illumina's NextSeq
500 and MiniSeq. The NextSeq 500
and the MiniSeq employ the latest enhancements in two-channel,
sequencing by synthesis (SBS) technology. 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 120 Gb generated per sequencing run. Both platforms
deliver high quality data with reduced cycle and data processing times due to the
two colour sequencing approach. The recent addition of the MiniSeq
(May, 2016) will permit greater flexibility in experimental design and faster turn-around-times
for smaller scale projects.
Sequencing Platform Comparison
| Applications | Amplicon, targeted RNA, small RNA, targeted gene panels, small genome | Exome, transcriptome, ChIP-Seq, targeted resequencing |
| Max Output | 7.5 Gb | 120 Gb |
| Max Read Length | 2x150 bases | 2x150 bases |
| Max Reads per Run | 25 million | 400 million |
| Run Time | 4-24 hours | 12-30 hours |
| Chemistry | 2 colour | 2 colour |
Services
- 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 Pearl Campbell to discuss
NGS Services, Pricing and Sample Submission Guidelines
- A 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 include a statement of work and a quotation.
- All NGS service requests must be entered in iLab and reference the Service Agreement
number provided when the project is initiated. Samples should be provided with a
copy of the sample submission form and a reference to the iLab request ID
- 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.
Library Construction
| Type | Protocol | Samples Per Run |
Cost per sample
Internal (OHRI / U of Ottawa)
|
Cost per sample
External
| Sample Submission Information |
| RNA | Illumina Stranded mRNA Prep | As required, up to 96 |
$333.00
|
Academic:
$366.00
Government:
$403.00
Industry/For profit:
$463.00
|
25 ng - 1.0 ug Total RNA in 25 ul nuclease free ultrapure water
Comments:
For mRNA using poly-A selection.
Protocol has been optimized for quality RNA as assessed on the Fragment Analyzer. RIN = 8.
|
| RNA | Illumina Stranded Total RNA Prep | As required, up to 96 |
$409.00
|
Academic:
$450.00
Government:
$495.00
Industry/For profit:
$570.00
|
25 ng - 1.0 ug Total RNA in 40 ul nuclease free ultrapure water
Comments:
For mRNA and ncRNA, excluding miRNA using Ribo-depletion.
Protocol has been optimized for quality RNA as assessed on the Fragment Analyzer. RIN = 8.
|
| RNA | NEBNext Ultra II Directional mRNA (poly-A) | As required, up to 96 |
$295.00
|
Academic:
$324.00
Government:
$356.00
Industry/For profit:
$410.00
|
5 ng - 1 µg Total RNA (poly(A) mRNA workflow) in 40 ul nuclease free ultrapure water
Comments:
For mRNA using poly-A selection.
Low input
|
| RNA | NEBNext Ultra II Directional Total RNA (Ribo-depletion) | As required, up to 96 |
$353.00
|
Academic:
$389.00
Government:
$428.00
Industry/For profit:
$492.00
|
10 ng - 1 µg Total RNA (Human/Mouse/Rat ribosomal depletion workflow) in 11 ul nuclease free ultrapure water
Comments:
For mRNA using poly-A selection.
Low input
|
| Small RNA | NEBNext Small RNA | As required |
$321.00
|
Academic:
$353.00
Government:
$389.00
Industry/For profit:
$447.00
|
100 ng - 1 µg Total RNA in max 6 ul nuclease free ultrapure water
Comments:
For small RNA, magnetic size-selection targets 21nt miRNA and 30nt piRNA.
|
| Small RNA | Lexogen Small RNA | As required |
$385.00
|
Academic:
$424.00
Government:
$466.00
Industry/For profit:
$536.00
|
50 pg to 1,000 ng Total RNA
Comments:
Optimized for low RNA content samples
|
| DNA | Illumina Nextera XT | As required, up to 384 |
$270.00
|
Academic:
$297.00
Government:
$326.00
Industry/For profit:
$375.00
|
1 ng gDNA in 5 ul nuclease free ultrapure water
Comments:
DNA is simultaneously fragmented and tagged with sequencing adapters in a single tube enzymatic reaction. Nextera XT supports ultra-low DNA input of only 1 ng. It enables a wide range of input samples, including small genomes, PCR amplicons greater than 300 bp, plasmids, microbial genomes, concatenated amplicons, and double-stranded cDNA.
|
| DNA | Illumina DNA Prep | As required, up to 384 |
$280.00
|
Academic:
$308.00
Government:
$339.00
Industry/For profit:
$390.00
|
Recommended input 100 ng gDNA, (can support 1–500 ng)
Comments:
DNA is simultaneously fragmented and tagged with sequencing adapters in a single tube enzymatic reaction, multiple sample types, and both small and large genomes.
|
| DNA | NEBNext Ultra II DNA | As required, up to 96 |
$250.00
|
Academic:
$275.00
Government:
$303.00
Industry/For profit:
$348.00
|
500 pg - 1 ug of fragmented DNA in max 50 ul 0.1X TE
Comments:
For as little as 500 picograms of input DNA, Prepare libraries from ALL your samples, including GC-rich DNA and FFPE DNA samples
|
Library Sequencing
| Next Generation Sequencing | Run Module | Approximate Reads per Run |
Cost per sample
Internal (OHRI / U of Ottawa)
|
Cost per sample
External Academic
|
Cost per sample
External Government
|
Cost per sample
External Industry / For profit
|
| MiniSeq | 75 Cycle High Output | 25M |
$2,194.00
|
$2,414.00
|
$2,655.00
|
$3,054.00
|
| 150 Cycle High Output | 25M |
$2,443.00
|
$2,687.00
|
$2,956.00
|
$3,399.00
|
| 300 Cycle High Output | 25M |
$3,485.00
|
$3,833.00
|
$4,217.00
|
$4,849.00
|
| 300 Cycle Mid Output | 8M |
$1,706.00
|
$1,876.00
|
$2,064.00
|
$2,374.00
|
| NextSeq 500 | 75 Cycle High Output | 400M |
$3,365.00
|
$3,702.00
|
$4,072.00
|
$4,683.00
|
| 150 Cycle High Output | 400M |
$5,873.00
|
$6,460.00
|
$7,106.00
|
$8,172.00
|
| 300 Cycle High Output | 400M |
$8,927.00
|
$9,820.00
|
$10,802.00
|
$12,422.00
|
| 150 Cycle Mid Output | 130M |
$2,737.00
|
$3,011.00
|
$3,312.00
|
$3,809.00
|
| 300 Cycle Mid Output | 130M |
$3,916.00
|
$4,307.00
|
$4,738.00
|
$5,449.00
|
- A charge of $150 will be added for bioinformatics pre-processing and demultiplexing to single-cell sequencing runs
Deliverables and Results Retrieval
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://support.illumina.com/help/BaseSpace_Sequence_Hub/Source/Informatics/BS/TransferOwner_swBS.htm
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.
Next Generation Sequencing Resources
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:
Mailing Address
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
Contact Information
Caroline Vergette
cvergette@ohri.ca
613.737.8899 x73251 (lab phone)
613.739.6294 (fax)
Pearl Campbell
pcampbell@ohri.ca
613.737.8899 x73110 (office)
