Genomics Core

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, NextSeq, and iSeq instruments. We recommend consultation with Genomics Core 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 Genomics Core effort as per our fee structure. All samples are assumed to be safe and no greater than BSL1, unless otherwise agreed upon in advance.

User rates subject to change without notice or as material costs change. Troubleshooting may necessitate additional costs.

Services

• DNA Extraction
• Genome and Metagenome Library Preparation
• Metabarcoding of Amplicon Products
• RNA Seq
• Illumina NovaSeq Sequencing
• Illumina iSeq Sequencing
• Illumina NextSeq Sequencing

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

Contact us at genomicscore@utk.edu.

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.

	Internal UT User	External Academic	External Non-Academic
Manual extraction, up to 100 samples, each	$14	$18	$21
Manual extraction, more than 100 samples, each	$12	$15	$18
Automated extraction, 24 to 48 samples, each, 24 sample minimum	$10	$12	$14
Automated extraction, 49 to 96 samples, each	$8	$10	$12
Automated extraction, more than 96 samples, each	$6	$8	$10

 

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 50-250 ng of DNA in less than 15 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 Illumina sequencing option.

	Internal UT User	External Academic	External Non-Academic
Genome and metagenome preps, 1-11 samples, each	$65	$82	$100
Genome and metagenome preps, 12-48 samples, each	$53	$67	$82
Genome and metagenome preps, >48 samples, each	$42	$53	$65

 

Metabarcoding of Amplicon Products

Amplicon libraries are prepared with Illumina’s two-step PCR 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.  We offer primer optimization and custom PCR setups when appropriate. Please contact Core staff prior to preparing your own library to confirm compatibility with Illumina sequencing platforms, as specific adapters are required.

The costs below for library construction of extracted, quantified DNA. Most costs are for batches of samples prepared at once. We offer 16S amplicon sequencing at the individual sample scale. For full library prep, DNA should be diluted to 10 ng/ul, with 10 ul provided. Next you will need to select the appropriate Illumina sequencing option.

	Internal UT User	External Academic	External Non-Academic
Full Amplicon library prep, up to 24 samples	$1,050	$1,325	$1,625
Full Amplicon library prep, 25-48 samples	$1,300	$1,625	$2,000
Full Amplicon library prep, 49-96 samples	$1,700	$2,125	$2,550
Full Amplicon prep of single 16S sample	$45	$57	$68
Amplicon library prep of post-PCR product, up to 24 samples	$800	$1,000	$1,225
Amplicon library prep of post-PCR product, 25-48 samples	$1,000	$1,250	$1,550
Amplicon library prep of post-PCR product, 49-96 samples	$1,350	$1,700	$2,025
Primer Optimization fee	$300	$375	$450
Individual PCR only, up to 24 samples	$175	$225	$275
Individual PCR only, 25-48 samples	$200	$250	$300
Individual PCR only, 49-96 samples	$288	$360	$435

 

RNA Seq

RNA libraries are prepared using Zymo Research’s Zymo-Seq RiboFree Total RNA Library Kit, which can include 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 Illumina sequencing option.

	Internal UT User	External Academic	External Non-Academic
RNA prep of up to 12 samples, each	$95	$120	$145
RNA prep of 13-48 samples, each	$85	$110	$130
RNA prep of >48 samples, each	$75	$95	$115

 

Illumina iSeq Sequencing

The Illumina iSeq is a small next-generation sequencer that can produce a maximum of 4 million read pairs (clusters). It is ideal for very small sequencing projects and test runs for larger sequencing projects. The costs below are for PREPARED libraries. Costs for library prep done at the core facility listed on this website are in addition to the cost of the flow cell.

Flow Cell	Read Length	SE Reads	PE Reads	Internal UT	External Academic	External Non-Academic
300 cycle	2×150 nt	~4 M	~8 M	$790	$840	$890
iSeq run only				$100	$150	$200

M: million reads, B: billion reads, SE: single-end, PE: paired-end
 

Illumina NextSeq Sequencing

The Illumina NextSeq 1000 uses a patterned flow cell technology to sequence up to 400 million read pairs (clusters). It replaces our previous Illumina MiSeq, with similar capabilities at reduced costs and higher quality. It is ideal for small to medium sized sequencing projects. Lane sharing may be available for small projects. Contact Core facility staff for information.

The costs below are for PREPARED libraries. Costs for library prep performed at the Core facility listed on this website are in addition to the cost of the flow cell. Custom read lengths are also available, generally requiring whole flow cell reads. The appropriate NextSeq 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.

Flow Cell	Read Length	SE Reads	PE Reads	Internal UT	External Academic	External Non-Academic
P1 100	2×50 nt	~100 M	~200 M	$1,070	$1,220	$1,370
P1 300	2×150 nt	~100 M	~200 M	$1,370	$1,520	$1,670
P1 600	2×300 nt	~100 M	~200 M	$1,930	$2,080	$2,230
P2 100	2×50 nt	~400 M	~800 M	$1,470	$1,620	$1,770
P2 200	2×100 nt	~400 M	~800 M	$2,500	$2,650	$2,800
P2 300	2×150 nt	~400 M	~800 M	$3,215	$3,365	$3,515
P2 600	2×300 nt	~400 M	~800 M	$3,470	$3,620	$3,770
Run costs only				$300	$450	$600

M: million reads, B: billion reads, SE: single-end, PE: paired-end
 

Illumina NovaSeq Sequencing

The NovaSeq 6000 is a large-scale sequencer from Illumina, generating up to 10 billion read pairs (clusters) 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 offer pooling options to reduce costs for users. Contact Core Facility staff for further information. Custom read lengths are also available, generally requiring whole flow cell reads.

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.

Flow Cell	Read Length	SE Reads	PE Reads	Internal UT	External Academic	External Non-Academic
SP 200	2 x 100 nt	~650-800 M	~1.3-1.6 B	$3,720	$4,135	$4,385
SP 300	2 x 150 nt	~650-800 M	~1.3-1.6 B	$4,015	$4,445	$4,695
SP 500	2 x 250 nt	~650-800 M	~1.3-1.6 B	$5,415	$5,925	$6,175
S1 200	2 x 100 nt	~1.3-1.6 B	~2.6-3.2 B	$6,175	$6,725	$6,975
S1 300	2 x 150 nt	~1.3-1.6 B	~2.6-3.2 B	$6,645	$7,215	$7,465
S2 200	2 x 100 nt	~3.3-4.1 B	~6.6-8.2 B	$11,035	$11,835	$12,085
S2 300	2 x 150 nt	~3.3-4.1 B	~6.6-8.2 B	$11,735	$12,575	$12,825
S4 200	2 x 100 nt	~8-10 B	~16-20 B	$15,630	$16,670	$16,920
S4 300	2 x 150 nt	~8-10 B	~16-20 B	$17,355	$18,485	$18,735
NovaSeq run only				$500	$750	$1,000

M: million reads, B: billion reads, SE: single-end, PE: paired-end

The Genomics Core houses additional equipment available for use.

• Pippen Prep
  • The Pippin Prep performs automated gel extraction. and is available for both assisted and unassisted use. Contact Core staff for information on available cassettes.
• Bioruptor
  • The Bioruptor uses ultrasound to fragment DNA and is available for both assisted and unassisted use.
• Bioanalzyer
  • The Agilent Bioanalzyer quantifies and qualifies DNA and RNA.  The appropriate chip is determined by the expected product size and concentration.  Chips hold either 11 or 12 samples.
• Bench Fee
  • Users may reserve clean room bench space to perform their own lab work. Non-filtered tips and pipets will be provided. If any training or staff involvement is required, additional costs may be necessary, at the staff labor rate. Contact Core facility staff for more information.

	Internal UT User	External Academic	External Non-Academic
Pippin Prep, unassisted (a)	$10*	$16*	$20*
Pippin Prep, assisted (b)	$45*	$69*	$90*
Pippin Prep, cassettes	$65	$65	$65
Bioruptor, unassisted (a)	$10	$16	$20
Bioruptor, assisted (b)	$20	$31	$40
Bioanalyzer, High Sensitivity chips, 11 samples max	$75	$115	$150
Bioanalyzer, standard sensitivity chips, 12 samples max	$60	$92	$120
Labor, Manager	$45	$69	$90
Hourly bench fee, no staff involvement	$10	$15	$20

(a)  Unassisted use implies that the user has been previously trained on the instrument and is capable of performing all needed tasks without assistance from Core facility personnel
(b)  Assisted use implies that the user has not received instrument training and will require assistance from Core facility personnel for sample analysis
*Plus $65 for cassette costs, if not provided by the user

User rates subject to change without notice or as material costs change. Troubleshooting may necessitate additional costs.

The UTGC no longer offers Sanger Sequencing in house. Sanger Sequencing must be sent off campus. We offer drop boxes across campus for those researchers wishing to mail in their samples for Sanger sequencing. Samples are mailed overnight to Eurofins Genomics with results returned by, or before, noon the next day. The quality of your results is dependent upon the quality of DNA that you submit to Eurofins, so it is critical that you follow their directions in sample preparation and sample labeling (request free bar codes).

The current price for Eurofins Sanger sequencing is $4.00/tube or $3.00/well for 96-well plates, as well as $1.00/sample for Load Only samples. Eurofins offers >70 universal sequencing primers for free with your sequencing order. Results (.seq and .ab1 files) will be returned the next day before noon, including on Saturday.

Samples can be dropped off for free shipping on the Ag campus at this location:

• The UTIA Omics Hub Lab, Plant Biotechnology Building, Room 308 (contact info: Sujata Agarwal; sagarwal@utk.edu; 865-974-0676)

Some individual orders qualify for free shipping. See details here.