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We are now operational. For product and service inquiries, please contact us at: ngsf@usask.ca.

Capabilities

  • NGS applications that researchers could use include:
    • gene expression (RNAseq) – which genes are expressed and at what level
    • chromatin immunoprecipitation (ChIP) & sequencing (ChIPseq) – which gene promoters are bound and thus regulated by a transcription factor
    • methylation (MeDIPseq) – methylated DNA immunoprecipitation sequencing to identify methylated nucleotides important in controlling gene expression
    • genome sequencing – complete characterization of the entire genome of a particular species
    • disease gene identification – identification of variants or mutations associated with disease e.g. cancer
    • deconvolution of pooled library screens (shRNA and CRISPR) – to identify the shRNA or CRISPR targeting sequences present in samples to determine which genes are knocked down or knocked out, respectively, in these high-throughput experiments
    • deconvolution of phage-display library sequences to identify antibody binders
    • deconvolution of barcode libraries to track clonal evolution

Staff

Austin Hammond - NGSF Research Officer

Roles and Responsibilities:

  • The primary purpose of this position is to oversee the operation of the NGSF and provide technical and scientific support to the users of this facility.
  • The position involves developing experimental protocols, instructing and training users in advanced procedures, and interpreting data and maintaining instruments in research-ready operating mode.
  • The research officer will maintain close contact with the users of the NGSF, be responsive to their needs and engage in research collaborations with the faculty utilizing NGSF instrumentation for their research.

Contact information:

Austin Hammond

Lab: B128
Office: B109D
Phone: 306-966-1846
Health Sciences Building, 107 Wiggins Road, Saskatoon, SK S7N 5E5

E-mail: austin.hammond@usask.ca

Re: May 1, 2019 Launch and Learn session from Illumina

To obtain copies of the slides presented, please contact Austin Hammond or Deborah Anderson (deborah.anderson@saskcancer.ca).

Shared Equipment - No Fees

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.

Note that, priority for use will be given to the NGSF Research Officer, Austin Hammond, since this equipment was acquired to support NGSF applications.

Thus, if necessary Austin may need to contact users that have booked time to reschedule their time if he needs to carry out time-sensitive analyses for NGS applications.

As much notice as possible will be given.

  • No fees to use.
  • User supplies consumables, but only the appropriate equipment-specific consumables are to be used.

Quantitative Real-Time PCR


Applied Biosystems StepOne Plus

  • Quantitative mRNA expression level measurements
  • To arrange the required orientation and/or training prior to first use, please contact Austin Hammond (austin.hammond@usask.ca)
  • Users must purchase the appropriate reagents that are compatible with this machine, specifically these exact 96-well plates and seals:

qPCR platesqPCR seals

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

Services Available - Fees Apply

Bioanalyzer

TapeStation 4150 Bioanalyzer from Aglient

  • For determining sample quality
    • e.g. total RNA, prior to RNAseq library preparation.
    • e.g. after RNAseq library preparation, prior to pooling libraries to run NGS
  • Each tape has 16 lanes and 1 lane of standards is required with each batch of samples.
  • Clients can use the unused lanes on the same tape at a different time to run additional samples, reserving 1 lane of standards per run.
                Assay
          Limit of detection
          Size range
          1 to 15 samples*
         16 to 32 samples
               RNA
               5 ng/ul
               N/A
             $146.53
               $270.56
   High Sensitivity RNA
             100 pg/ul
               N/A
             $162.36
               $302.22
         DNA (D1000)
        0.1 ng/ul (single peak)
        35 – 1000 bp
             $131.77
               $241.04
High Sensitivity DNA (D1000 HS)
           5 pg/ul (single peak)
        35 – 1000 bp
             $172.51
               $322.52

*Includes 1 standard per tape and processing time.

 

Qubit

  • For highly accurate determination of sample quantity
    • e.g. total RNA, prior to RNAseq library preparation.
    • e.g. after RNAseq library preparation, prior to pooling libraries to run NGS
                   Assay
            Limit of detection
            Upper limit
       First sample*
Each sample after first, up to 24
         dsDNA Broad-Range
               100 pg/ul
           1000 ng/ul
           $28.02
              +$2.56
         dsDNA High Sensitivity
                 10 pg/ul
            100 ng/ul
           $28.02
              +$2.56
           RNA High Sensitivity
               250 pg/ul
            100 ng/ul
           $28.02
              +$2.56

*Includes the required 2 standards and the processing time.

 

 

KingFisher

  • Semi-automated DNA and RNA isolations from bacteria, tissue culture cells, tissue, blood (e.g. circulating tumor DNA), saliva, paraffin-embedded tissue sections.
  • Information regarding input samples and fees yet to be determined.

Next Generation Sequencing

  • NextSeq 550; Read output = 320 - 400 M reads; Maximum MB output = 120,000 MB
  • iSeq 100; Read output = 3.2 - 4 M reads; Maximum MB output = 1200 MB
  • Determine how the Next Generation Sequencing Facility might facilitate your research.
  • Please contact Austin Hammond to discuss your project needs:
  • Obtain a quotation for the NGS work                                   

Next   i

Bioinformatics

 

Austin also has expertise in Bioinformatics analysis.

His services are availabale on a cost recovery basis for his time working on your bioinformatics project.

Discuss your project objectives and obtain an estimate for these services.