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The Next-Generation Sequencing Facility (NGSF) is a high-throughput genomics facility located at the University of Saskatchewan. The primary goal of the NGSF is to further basic and clinical research by providing access to high-throughput sequencing technologies and expertise.

In addition to library preparation and sequencing services, data analysis and bioinformatics services are also available, either together or each independently. The NGSF is not a clinically-certified laboratory and all results are provided on a research basis.

Contact us to discuss your project objectives and obtain a service quote.

High-throughput Sequencing

Library types

We offer library preparation services for a variety of research applications, including:

  • Whole-genome sequencing (WGS)
  • Whole-transcriptome sequencing (RNA-Seq)
  • Chromatin immunoprecipitation (ChIP-Seq)
  • Targeted gene panels for SNP or mutation detection
  • Small genome (microbial, viral) and plasmid sequencing
  • Single-cell sequencing applications

Contact us to discuss preparation of other library types and sequencing approaches.

Platforms

The NGSF currently operates two Illumina sequencing platforms and one 10x Genomics single cell analysis system : NextSeq 550, iSeq 100 and Chromium IX

Platform and key applications Sequencing kit(s)

NextSeq 550

  • Gene expression profiling/whole-transcriptome shotgun sequencing (RNA-Seq)
  • Whole-genome sequencing (WGS)
  • Exome sequencing
  • Chromatin immunoprecipitation sequencing (ChIP-Seq)
  • Whole-genome bisulfite sequencing (WGBS) for analysis of DNA methylation
  • Shotgun metagenomics
  • Illumina BeadChip microarrays (cytogenetic and genotyping)

Mid Output

2x75 or 2x150 bp reads

110-130 million read pairs

High Output

1x75, 2x75, or 2x150 bp reads

320-400 million read pairs

 NextSeq 550

iSeq 100

  • Targeted gene panels (e.g. cancer hotspot, custom SNP)
  • Small genome sequencing (microbial, viral)
  • Plasmids and long-range amplicon sequencing
  • 16S ribosomal sequencing for microbial community profiling

i1

2x150 bp reads

3.2-4.0 million read pairs

 iSeq 100

Chromium iX

  • Single cell gene expression
  • Single cell ATAC (Assay for Transposase Accessible Chromatin)
  • Single cell immune profiling
  • Single cell multiome ATAC + gene expression
  • Single cell FIXED RNA profiling

 

Chromium iX

Bioinformatics

Routine and custom services

The NGSF offers bioinformatic and computational biology services for human and non-human data, including:

  • Differential expression
  • Pathway analysis
  • De novo genome and transcriptome assembly
  • Genome and transcriptome annotation
  • Candidate biomarker identification
  • Somatic and germline variant calling
  • Data submission to sequence data repositories (e.g. NCBI SRA)
  • Custom qPCR assay design and development

These services may be added to a sequencing project undertaken at the NGSF or as independent projects.

Contact us to discuss available bioinformatic services and to obtain a project cost estimate.

Sample Isolation and Analysis

Agilent TapeStation 4150

  • Successor to the Agilent Bioanalyzer
  • Determine RNA and DNA sample integrity (RIN, DIN)
  • Measure DNA sample or sequencing library fragment lengths
  • Each tape has 16 lanes and 1 lane of standards is required with each batch of samples
  • Unused lanes on the same tape may be used within two weeks to run additional samples at a reduced rate, reserving 1 lane of standards per run
  • Prior Qubit quantification is recommended to ensure your sample concentrations do not overload the assay and result in poor assay performance
Assay
Limit of detection
Size range
1 to 15 samples*
RNA
5 ng/µl
N/A
$189
High Sensitivity RNA
100 pg/µl
N/A
$214
DNA (D1000)
0.1 ng/µl (single peak)
35 to 1000 bp
$172
High Sensitivity DNA (D1000 HS)
5 pg/µl (single peak)
35 to 1000 bp
$218
High Sensitivity DNA (D5000 HS)
5 pg/µl  (single peak)
100 to 5000 bp
$218
Genomic DNA
10 ng/µl
200 bp to > 60 kbp
$219

*Includes 1 standard per tape and processing time.

Qubit 4 Fluorometer

  • Highly accurate determination of DNA, RNA, or protein quantity
  • 1-20 µl sample required per assay
  • Spectrophotometric methods (e.g. NanoDrop) frequently overestimate nucleic acid concentration due to the influence of contaminants
  • Also available for use as shared equipment
Assay
  Limit of detection*
  Upper limit
  Standards (required)
  Each reading, up to 24
dsDNA Broad-Range
  100 pg/µl
  1000 ng/µl
  $12
  $5
dsDNA High Sensitivity
  10 pg/µl
  100 ng/µl
  $12
  $5
RNA Broad-Range
  1 ng/µl
  1000 ng/µl
  $12
  $5
RNA High Sensitivity
  250 pg/µl
  100 ng/µl
  $12
  $5

*For 20 µl sample input

ThermoScientific KingFisher Duo Prime

  • Semi-automated DNA and RNA isolation from bacteria, tissue culture cells, tissue, blood (e.g. circulating tumor DNA), saliva, paraffin-embedded tissue sections
  • Fees vary by sample type - please contact us for details

Shared Equipment

Guidelines for use

This equipment is available to use with no fees after users have received the required orientation/training on the use of the equipment and have completed a User Agreement.

Priority for use is given to NGSF staff to support facility operations. Users with conflicting bookings will be contacted as early as possible to reschedule.

Users must supply all consumables, and only approved equipment-specific consumables may be used.

Contact us to arrange the required orientation and training prior to first use.

Applied Biosystems StepOne Plus Quantitative Real-Time PCR

  • Targeted transcript and genomic copy-number quantification
  • Most-accurate quantification of sequencing library fragments
  • Quantify enrichment following chromatin immunoprecipitation (ChIP)
  • Four-colour system
    • FAM™/SYBR® Green
    • VIC®/JOE™
    • NED™/TAMRA™
    • ROX™

Approved consumables:
Applied Biosystems MicroAmp Optical Adhesive Film (4311971)
Applied Biosystems MicroAmp Fast Optical 96-Well Reaction Plate, 0.1 mL (4346906, 4346907)

Note: an identical Applied Biosystems StepOne Plus system is available to use in the Cancer Cluster in 4D40, HSc here.

Contact us to discuss design and development of custom qPCR assays.

Qubit 4 Fluorometer

  • Highly accurate determination of DNA, RNA, or protein quantity
  • Spectrophotometric methods (e.g. NanoDrop) frequently overestimate nucleic acid concentration due to the influence of contaminants
  • Qubit measurements are also available as fee-for-service

Approved consumables:
Invitrogen Qubit Assay Tubes (Q32856)

Please contact the Research Officer regarding availability at least 48 hours prior to desired use.

Members

Dr. Deborah Anderson, Director

Dr. Anderson provides guidance to the facility in addition to her roles as Director of Research and Senior Research Scientist at the Saskatchewan Cancer Agency and Professor in Oncology and Associate Member in Biochemistry, Microbiology and Immunology in the College of Medicine at the University of Saskatchewan.

Pashupati Bhandari, PhD, Research Officer

The Research Officer oversees operation of the NGSF, provides technical and scientific support, and engages in research collaborations with faculty utilizing NGSF instrumentation for their research.

Shahina Hayat, Bioinformatics Analyst

Shahina provides bioinformatics support to NGSF users and Saskatchewan Cancer Agency researchers.

Sudipta Dutta, Research Assistant

Sudipta provides support for the laboratory operations of the NGSF

Alumni

S. Austin Hammond, Research Officer

Aren Boulet, Research Assistant

Kristen Mitzel, Research Assistant

Daniel Udenze, PhD., Research Officer

Address

Lab: B128
Office: 1B25
Health Sciences Building, University of Saskatchewan
107 Wiggins Road
Saskatoon, SK
S7N 5E5