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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

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

Platforms

The NGSF currently operates two Illumina sequencing platforms: a NextSeq 550 and an iSeq 100.

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

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, reserving 1 lane of standards per run
Assay
Limit of detection
Size range
1 to 15 samples*
RNA
5 ng/ul
N/A
$164
High Sensitivity RNA
100 pg/ul
N/A
$180
DNA (D1000)
0.1 ng/ul (single peak)
35 to 1000 bp
$151
High Sensitivity DNA (D1000 HS)
 5 pg/ul (single peak)
35 to 1000 bp
$191
Genomic DNA
10 ng/ul
200 bp to > 60 kbp
$212

*Includes 1 standard per tape and processing time.

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
  • 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/ul
  1000 ng/ul
  $12
  $4
dsDNA High Sensitivity
  10 pg/ul
  100 ng/ul
  $12
  $4
RNA Broad-Range
  1 ng/ul
  1000 ng/ul
  $12
  $4
RNA High Sensitivity
  250 pg/ul
  100 ng/ul
  $12
  $4

*Includes the required 2 standards and the processing time

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.

Staff

Austin Hammond, Research Officer

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

Lab: B128
Office: GB37
Health Sciences Building, University of Saskatchewan
107 Wiggins Road
Saskatoon, SK
S7N 5E5