High-Throughput Sequencing

UT Genomics Core Facility

The UT Genomics Core (UTGC), along with the Center for Biotechnology (CEB) and the Office of Research, Innovation, and Economic Development (ORIED), are pleased to announce the arrival of the Illumina NovaSeq high throughput sequencing system.  

Service Overview

The UT Genomics Core provides high-throughput next-generation sequencing services to all interested on-campus and off-campus researchers. Sequencing is performed using the Illumina NovaSeq, MiSeq, or Oxford Nanopore MinION instruments located in room 407 of the Science and Engineering Research Facility (SERF) within the Center for Environmental Biotechnology (CEB). We recommend consultation with UTGC staff prior to project initiation. While we strive for successful sequencing every time, we cannot guarantee project success, and in all cases, the user will be billed for cost and labor for UTGC effort as per our fee structure. All samples are assumed to be safe and no greater than BSL1, unless otherwise agreed upon in advance.  Contact us at genomicscore@utk.edu.

Project Workflow

1

DNA/RNA extraction
Nucleic acid is extracted and purified

2

Library Prep
Prepare sample for sequencing by adding appropriate adapters

3

Sequencing
Read the sequence of the sample and create raw data

4

Analysis
3 Steps: Primary and secondary analysis, and interpretation

The prices listed below are subject to change as material costs change. Troubleshooting may necessitate additional costs.  Click here to download a pdf version of the price list for UT users, external academic or non-profit users, and external non-academic users (commercial).

DNA Extraction

Some DNA extractions are suitable for automation and some are better suited for manual extraction. Automated extractions are performed on a KingFisher Flex using Zymo Research kits and manual extractions are performed using Qiagen extraction kits.  Please contact Core Facility staff to discuss which method is best for your sample type.

Cost/Pricing DetailsInternal University of Tennessee UserExternal academic userExternal non-academic user
Manual DNA extraction, each
$16.00$20.00$30.00
Automated DNA extraction, 1-48 samples, each$13.00$20.00$39.00
Automated DNA extraction, 49-96 samples, each$7.00$11.00$20.00

 

Genome and Metagenome Library Preparation

Genome and metagenome libraries are prepared using Illumina’s DNA Prep kit (formerly Nextera DNA Flex Library Prep). The starting material needed is 100-500 ng of DNA in less than 30 uL volume, diluted in Tris-HCl, pH 8. The DNA should have an absorbance of 260/280 in the 1.8-2 range and 260-230 in the 2-2.2 range. Contact Core Facility staff if your template DNA does not meet these specifications. 

The costs below are for library construction of extracted, quantified DNA.  Next you will need to select the appropriate MiSeq or NovaSeq run.

Cost/Pricing DetailsInternal University of Tennessee UserExternal academic userExternal non-academic user
Genome and metagenome preps, 1-11 samples, each
$94.00$142.00$282.00
Genome and metagenome preps, 12-22 samples, each
$85.00$128.00$255.00

Metabarcoding of Amplicon Products

Amplicon libraries are prepared with Illumina’s two-step PCR Nextera XT amplicon protocol.  Users can prepare their own PCR products or Core staff can fully prepare the amplicon libraries with common primers for 16S, ITS, and COI.  Please contact Core staff prior to preparing your own library to confirm compatibility with Illumina sequencing platforms, as specific adapters are required.  These are the costs for library construction of extracted, quantified DNA.  For full library prep, DNA should be diluted to 10 ng/ul, with 10 ul provided.  Next you will need to select the appropriate MiSeq or NovaSeq run.

Cost/Pricing DetailsInternal University of Tennessee UserExternal academic userExternal non-academic user
Full Amplicon library prep, up to 24 samples$1,138.00$1,450.00$1,878.00
Full Amplicon library prep, 25-48 samples$1,445.00$1,811.00$2,384.00
Full Amplicon library prep, 49-96 samples$1,907.00$2,334.00$3,147.00
Amplicon library prep of post-PCR product, up to 24 samples$890.00$1,085.00$1,469.00
Amplicon library prep of post-PCR product,  25-48 samples$1,133.00$1,376.00$1,869.00
Amplicon library prep of post-PCR product,  49-96 samples$1,511.00$1,788.00$2,493.00

RNASeq

RNA libraries are prepared using Zymo Research’s Zymo-Seq RiboFree Total RNA Library Kit, which includes an rRNA depletion step.  The minimum input amount of RNA is 100 ng, but the recommended input is 500 ng.  RNA should have A260/A280 and A260/A230 ratios >1.8 and be DNA-free.  Please check that this kit is compatible with your needs. 

The costs below are for library construction of extracted, quantified and quality confirmed RNA.  Next you will need to select the appropriate MiSeq or NovaSeq run.

Cost/Pricing Details Internal University of Tennessee User External academic user External non-academic user
RNA prep of up to 12 samples, each $141.00 $205.00 $350.00
RNA prep of 13-24 samples, each $129.00 $185.00 $300.00

Illumina MiSeq Sequencing

The Illumina MiSeq is a benchtop sequencer specialized for lower-output runs on single-lane flow cells, offering Illumina’s longest read length of up to 300 nucleotides, paired-end. The MiSeq is ideal for amplicon sequencing, such as for bacterial 16S rRNA, and small genomes.  It can also be used to test larger runs prior to running them on the larger Illumina NovaSeq. 

The appropriate Illumina MiSeq flow cell for your project is determined by the depth of coverage needed, as well as the desired read length.  Contact Core facility staff for advice on which flow cell is right for your project. The costs below are for a PREPARED library.  Costs for library prep done at the Core facility listed on this website are in addition to the cost of the flow cell.

MiSeq ServiceInternal University of Tennessee UserExternal academic userExternal non-academic user
Version 3, 600 cycle (2 X 300) kit; ~22-24 million read pairs
$1,975.00$2,200.00$2,980.00
Version 3, 150 cycle (2 X 75) kit; ~22-24 million read pairs
$1,380.00$1,500.00$2,160.00
Version 2, 500 cycle (2 X 250) kit; ~12-14 million read pairs
$1,660.00$1,800.00$2,630.00
Version 2, 50 cycle (2 X 25) kit; ~12-14 million read pairs
$1,000.00$1,200.00$2,010.00
MiSeq run only$350.00$400.00$600.00

Illumina NovaSeq Sequencing

The NovaSeq 6000 is the latest large-scale sequencer from Illumina, generating unprecedented output in less than two days using patterned flow cell technology, with scalable through-puts to accommodate most projects. Careful consideration of sample numbers and flow cell output is crucial for effective use of this platform. The high yields of the NovaSeq flow cells may present difficulties in efficiently filling flow cells for many researchers.  As such, we are currently offering the smallest flow cell, the SP, by single lane use.  We hope to expand our options in the future.  Custom options may be available upon request.  Contact core staff for more information. 

The appropriate Illumina NovaSeq flow cell for your project is determined by the depth of coverage needed, as well as the desired read length.  Contact Core facility staff for advice on which flow cell is right for your project. The costs below are for a PREPARED library.  Costs for library prep done at the Core facility listed on this website are in addition to the cost of the flow cell.

For assistance calculating coverage necessary for your specific project, visit Illumina’s Coverage Calculator.

NovaSeq ServiceInternal University of Tennessee UserExternal academic userExternal non-academic user
SP flow cell lane 2 x 100 nt Sequencing, ~300-400 million read pairs
$2,200.00$2,800.00$4,000.00
SP flow cell lane 2 x 150 nt Sequencing, ~300-400 million read pairs
$2,356.00$3,100.00$4,500.00
SP flow cell lane 2 x 250 nt Sequencing, ~300-400 million read pairs
$3,000.00$3,900.00$5,000.00

Applications for Illumina MiSeq and NovaSeq high-throughput sequencing include:

  • Genome Sequencing
  • RNA Sequencing
  • Metagenomics
  • 16S Metabarcoding
  • Custom Amplicon Sequencing  

Users may build their own libraries or Genomics Core staff can assist with library preparation. Students are encouraged to participate in lab work associated with their individual projects.

Oxford MinION

The Oxford MinION sequencer enables direct, real-time analysis of short to ultra-long (>4 Mb) fragments of DNA/RNA in an easy-to-use, low-cost format.

Oxford Nanopore MinION Applications

  • Whole genomes/exomes
    Metagenomics
  • Targeted sequencing
    Whole transcriptome (cDNA)
  • Smaller transcriptomes (direct RNA)
  • Multiplexing for smaller samples

Oxford MinION Pricing

Cost/Pricing Details Internal University of Tennessee User External academic user External non-academic user
Library Prep with Oxford Nanopore Rapid Sequencing Kit, per sample $150.00 $173.00 $248.00
Library Prep with Oxford Nanopore Genomic DNA Litigation Kit, per sample $225.00 $256.00 $371.00
Oxford Nanopore MinION run* $45.00 $68.00 $74.00
Oxford Nanopore wash between runs run* $32.00 $36.00 $40.00

*Flow cells for the MinION have the potential to be reused but have carryover between runs. For this reason, flow cells must be purchased by each individual user who have the option to reuse their own flow cells. Contact Core Facility staff for more information and flow cell costs.

Services Contact

For further information on applications, project design, and pricing, please contact Veronica Brown at GenomicsCore@utk.edu or 865-974-8080.  Please contact Core staff prior to beginning a project to ensure compatibility with the Illumina MiSeq.

For assistance with Illumina data processing:

The CEB Bioinformatics Resource Center (BRC) provides access to computational resources and expert advice for assembling and analyzing Illumina data. The BRC is located in SERF 736.

Access to DNAStar Software

DNAStar is a powerful bioinformatics software package that provides sequence analysis, cloning and primer design as well as next-gen sequencing, gene expression, RNA-Seq, ChIP-Seq, and transcriptome analyses. This software is paid for by the Center for Environmental Biotechnology and the Departments of Microbiology, Ecology and Evolutionary Biology, Biochemistry & Cellular and Molecular Biology, and Genome Science & Technology. Faculty, staff, and students within these departments are provided free access to DNAStar.

If other departments or individual labs wish to gain access, please contact Steven Ripp (saripp@utk.edu; 865-974-9605) to discuss payment options. Both PC and Mac versions are available. You can download a 14-day trial of DNAStar if you would like to test it before using.

For further information on applications, project design, and pricing, please contact Veronica Brown at GenomicsCore@utk.edu or 865-974-8080. Results include powerful, real-time, long-read sequencing of DNA and RNA