Service price list for NSHE institutions

Effective July 1, 2020

Unlisted services and pricing
Service Rates for NSHE-affiliated institutions
Unlisted services (consultations with the core director are always free) $50.00 / hour
Qiagen orders and pricing
Service Rates for UNR only
Qiagen orders: 5% discount for most items and free 2-day shipping; order as many items as you need and the fee is $20.00; email genomics@unr.edu with catalog number(s) and qty. $20.00 / order; any number of items per order
Sanger sequencing services and pricing
Service Rates for NSHE-affiliated institutions
Sanger sequencing $2.00 / sample
Fragment analysis services and pricing
Service Rates for NSHE-affiliated institutions
Fragment analysis setup: dilute (if needed), add standard and formamide $1.00 / sample
Fragment analysis run: run prepared sample on capillary gel $1.00 / sample
Fragment analysis dilution optimization: client prepares plate ready to load directly onto capillary gel. Standards cannot be included in samples. Client interprets data. $5.50
Fragment analysis dilution optimization: we will create up to 6 dilutions of 8 samples of a panel and determine the best dilution to use for a capillary gel run. Standards are not added to samples. $10.00 / panel
Illumina services and pricing (see two workflow examples for Illumina sequencing)
Service Rates for NSHE-affiliated institutions
Start NextSeq 500 sequencing run $100.00 / run
Start NextSeq 2000 sequencing run $150.00 / run
Start MiniSeq sequencing run $75.00 / run
Validate pooled library concentration by qPCR $45.00 / pool
Library pooling service using qPCR (already included in library preps done by NGC) $20.00 + $5.00 / sample
Illumina library prep services and pricing – up to 16 samples – includes work to quantify and pool. Per-sample prices include the cost of the kit and thus are subject to change.
Service Rates for NSHE-affiliated institutions
Illumina TruSeq Nano (100-200 ng input gDNA) $250.00 + $45.00 / sample
Illumina TruSeq Nano PCR-Free (1-2 ug input gDNA) $250.00 + $45.00 / sample
Illumnia Stranded mRNA Prep (100 ng-1 ug input total RNA) $250.00 + $60.00 / sample
Illumina DNA Prep (formerly Nextera Flex) (1-500 ng input gDNA) $250.00 + $55.00 / sample

Please see details below about library prep scheduling. We will use other sequencing prep kits upon request. Consult with the Nevada Genomics Center – typically the cost will involve a kit purchase, hourly service fees to prepare libraries and the cost of doing the library pooling work. If there is enough interest for a particular kit, we are willing to consider making it part of our regular service offerings.

Illumina sequencing kits purchased through the Nevada Genomics Center (4% S&H not included). Prices are subject to change. We do not add overhead to the cost of these kits aside of S&H.
Instrument Kit type Cycles Sequencing kit cost
NextSeq 550 Mid output 150 $1,144.75
NextSeq 550 Mid output 300 $1,843.00
NextSeq 550 High output 75 $1,567.50
NextSeq 550 High output 150 $3,002.00
NextSeq 550 High output 300 $4,811.75
NextSeq 2000 P2 100 $1,349.00
NextSeq 2000 P2 200 $2,536.50
NextSeq 2000 P2 300 $3,363.00
NextSeq 2000 P3 50 $2,137.50
NextSeq 2000 P3 100 $3,087.50
NextSeq 2000 P3 200 $4,275.00
NextSeq 2000 P3 300 $5,700.00
MiniSeq Rapid high output 100 $997.50
MiniSeq High output 75 $874.00
MiniSeq High output 150 $1,021.25
MiniSeq High output 300 $1,638.75
MiniSeq Mid output 300 $584.25
Agilent TapeStation 4150 services and pricing
Service Rates for NSHE-affiliated institutions
ScreenTape RNA ladder (optional) $13.00
ScreenTape RNA, per sample $3.00
ScreenTape DNA 1000 ladder (optional) $11.00
ScreenTape DNA 1000, per sample $3.00
ScreenTape DNA 5000 ladder (required for every 15 samples) $11.00
ScreenTape DNA 5000, per sample $3.00
DNA quantification services and pricing
Service Rates for NSHE-affiliated institutions
Qubit HS DNA (max 100 ng, up to 48 samples) $1.50 / sample
dsDNA-specific plate assay (max 200 ng, at least 48 samples) $10.00; + $1.00 / sample
RNA quantification services and pricing
Service Rates for NSHE-affiliated institutions
Qubit HS RNA (max 100 ng, up to 48 samples) $1.50 / sample
RNA-specific plate assay (max 500 ng, at least 48 samples) $10.00; + $1.00 / sample
PCR cleanup service and QuantStudio 3 usage pricing
Service Rates for NSHE-affiliated institutions
PCR cleanup (ExoSAP) $2.00 / sample
QuantStudio 3 qPCR instrument usage (client must prepare plate) $12.00 / run

 


Illumina Sequencing workflow examples

We break down our Illumina services into key components to give you the flexibility to plan your experiments as you wish. Here are two typical workflows and their costs. These should serve as examples for you to think about what workflow works best for you. Check with us for an official project estimate.

mRNA-seq of 12 human samples for differential gene expression analysis
Item Units Total cost
Base rate for mRNA library prep 1 $250.00
Prepare 12 samples (includes pooling) 12 $720.00
Obtain sample size distributions 12 $36.00
Purchase NextSeq 2000 P2 100-cycle sequencing kit 1 $1,349.00
Start NextSeq 2000 sequencing run 1 $150.00
Total cost for all items $2,505.00
Sequencing of 16 metagenomic samples
Item Units Total cost
Base rate for Illumina DNA Prep (formerly Nextera Flex) 1 $250.00
Prepare 16 samples (includes pooling) 16 $880.00
Obtain sample size distributions 16 $48.00
Purchase NextSeq 2000 P2 100-cycle sequencing kit 1 $1,349.00
Start NextSeq 2000 sequencing run 1 $150.00
Total cost for all items $2,677.00

Further details about our services

Hourly service rate

This is the hourly labor rate for services not explicitly listed. Does not apply to consultations with the core director – this is always free. Basically, anything we do that requires lab work will incur this hourly rate.

Examples: sequencing library construction with a kit not listed, work performed to ensure optimal results with your samples, and custom services designed to support your project.

Qiagen orders

For University of Nevada, Reno researchers, we can order the majority of items in the Qiagen catalog at a 5% discount and free two-day shipping. You can order as many items as you want and we’ll include a $20.00 processing fee.

Sanger sequencing

Includes Sanger reaction setup, capillary gel run and basecalling. Includes addition of sequencing primer if requested. Upon request, includes addition of an additive that helps sequence through regions prone to secondary structures (e.g. hairpins) or sequences with high GC content.

Re-run policy: we will accept samples from you to re-run the Sanger reaction & capillary gel at no cost if your results are poor and performance of our internal controls is poor.

Please submit samples in 8 well strip tubes. Caps that are not attached to the tubes are preferred. Label each tube 1, 2, 3, … corresponding to the order of samples on your sheet. Write the order number on the side of the first tube of each strip.

Samples must be received by 2 p.m. Mon-Thurs for data delivery the following afternoon. Samples received after 2 p.m. Thursdays will be processed on Monday for data delivery Tuesday.

Fragment analysis sample preparation

This does not include the capillary gel run. We will dilute (or not) sample as specified, and add it to a formamide + LIZ 500 internal size standard master mix.

We stock only the LIZ 500 size standard; please contact us if you need to discuss the use of a different standard.

Fragment analysis sample run

We will run appropriately prepared sample (either by us or as provided by you) on our capillary gel and deliver FSA data files.

Often, we are able to start runs and deliver your data at the end of the day or early the next morning. The earlier you bring your samples, the more likely you’ll get same-day data, particularly if you need us to set them up first. Samples received after 3 p.m. may not be processed until the following morning.

Fragment analysis dilution optimization

It is useful to create a series of dilutions of a subset of your fragment analysis samples to determine the best dilution to use. Often this only needs to be done one time per panel, as long as your sample prep conditions remain consistent.

If you prefer to set up your dilutions, please do not include standard. We will load your samples exactly as you prepared them.

If you would like us to do a dilution test, we will take up to 8 of your samples per panel and create up to 6 dilutions, add formamide, and run. We will interpret the data to suggest an appropriate dilution, but you will receive the data to see for yourself.

Illumina – start sequencing run

This is the cost of starting any type of Illumina sequencing run with a pooled sequencing library of a determined concentration. The minimum concentration of a pooled library is 1 nM; 4 nM is strongly recommended. The sequencing kit price is separate.

We recommend quantification of a sample prior to starting a run; see below for details about this service. If you decide to quantify your library concentration on your own and tell us what it is, we will use this value, but the NGC is not responsible for any poor outcomes.

We require that the size distributions of all samples, or the library pool, is known prior to starting a run. If you do not have and want library size distribution data, the NGC is not responsible for any poor outcomes.

If an instrument or operator issue causes a run failure, the NGC will provide a replacement sequencing kit.

Inclusion of 1% PhiX is routine for post-sequencing quality checks. More PhiX can be included if requested, particularly for low diversity library pools.

Illumina – validate pooled library concentration

We will validate the effective concentration of your library. Effective concentration is related to the number of molecules able to form clusters on an Illumina flow cell.

We must know the size distribution of your library pool. If individual samples of a pool have a similar size distribution profile, it is not necessary to check the pool size distribution.

We include in the quantification run a library that was previously observed to cluster well. Whenever feasible, the chosen reference library was prepared using the same type of library prep kit and ran on the same Illumina instrument.

On occasion, if we are sequencing certain library types that have never been sequenced on our instruments, we may not guarantee meeting the expected yield as we don’t have the ability to use an appropriate reference library pool. We discuss this with you on a case-by-case basis.

Library Pooling Service

This is included in the price of our library prep services. We will use a quantification kit to quantify your library concentrations using the same standard curve. We must have library size information (e.g. from a Bioanalyzer run). Typically, your libraries are then pooled equimolarly, but you can instruct us otherwise.

Illumina library construction

We will use a commercially available kit to generate sequencing libraries from samples that you provide. If we do not stock a particular kit, please contact us to discuss how we can help. We have done many custom sequencing library preparations.

Currently we stock the following kits:

  1. Illumina TruSeq Nano with/without PCR: construct a shotgun library from DNA
    • For the PCR option: 100 ng for 350 bp inserts, 200 ng for 550 bp inserts
    • For the PCR-free option: 1 ug for 350 bp inserts, 2 ug for 550 bp inserts
    • Cost of Covaris shearing is included
    • We may recommend a Covaris shearing test with an extra sample to ensure compatibility with the shearing protocol. There is an extra fee for this.
  2. Illumina DNA Prep (formerly known as Nextera Flex): construct a library from most types of DNA using tagmentation
    • 1-500 ng input (min 100 ng for large genomes)
  3. QIAseq Stranded RNA Select: construct a polyA enriched mRNA library
    • 100 ng – 1 ug total RNA input (we prefer 500 ng)
    • ~500 bp average size inserts are the default; discuss with us if you need a different insert size

All sample prep service prices include:

  • Library quantification (required to aid in pooling)
  • Pooling of samples based on qPCR quantification

We must know the size distribution of samples before pooling with Bioanalyzer runs. This cost is not included and will depend on how many samples are processed.

Before starting a sequencing library prep project, we need the following information:

  • A230, A260 and A280 readings (e.g. from a NanoDrop). The NGC does not have the equipment to get these readings. There are several NanoDrops on campus; please contact us if you need to locate one.
  • Quantity of dsDNA or RNA must be determined using specific methods (e.g. Qubit); A260 values are not reliable for concentration determination
  • For mRNA library generation: assessment of total RNA quality for each sample
  • Other information may be requested based on project specifics.

PCR cleanup

Typically done for cleanup of PCR products prior to Sanger sequencing. Does not include prior dsDNA quantification of the PCR reaction. You provide us with PCR product straight off the thermocycler. Samples must be quantified for dsDNA concentration and large numbers of samples can instead be subsampled to obtain an average concentration to apply for all samples. An appropriate amount of PCR product is then treated with enzymes that degrade remaining PCR primers and dephosphorylate remaining dNTPs. This treated amount is then ready to go straight into a Sanger reaction with appropriate primer.

DNA quantification

Qubit dsDNA: 1-48 samples
Picogreen plate assay: 48 or more samples

Standards for plate-based assay

We use dyes specific for dsDNA binding for DNA quantification. By default, we will assay up to 48 samples with the Qubit. Any more than 48, or by your request, we’ll use a plate-based assay.

The upper measurement limit of the Qubit is 100 ng; for plate-based assays, 200 ng. We use 7 standards in triplicate for generating the plate-based assay standard curve.

Prepare your samples (dilute if necessary) and organize in numbered strip-caps. We routinely pipet 2 ul per sample, so you must provide a minimum volume of 3 ul. Upon request, we can pipet up to 10 ul for the plate assay and up to 20 ul for Qubit.

Try to ensure your samples are dilute enough such that we load <100 ng for Qubit and <200 ng for plate-based assays. You usually will know from experience, and you can request that we check a sample or two before submitting a large group of samples. The Qubit will not report a value if it is too high. The plate-based assay will report an uncertain value due to readings being outside the linear range of standards. We have to charge fees per usual if we re-run samples if they were initially too concentrated.

RNA quantification

Qubit RNA: 1-48 samples
Plate assay: 48 or more samples

Standards for plate-based assay

We use dyes specific for RNA binding for RNA quantification. By default, we’ll assay up to 48 samples with the Qubit. Any more than 48, or by your request, we’ll use a plate-based assay.

The upper measurement limit of the Qubit is 100 ng; for plate-based assays, 500 ng. Please see the DNA quantification section for relevant information for sample submission.

Agilent Bioanalyzer 2100 Runs

Our Agilent Bioanalyzer is available for custom projects, particularly if small RNA needs to be analyzed.  Please refer to the TapeStation information for your needs.

TapeStation 4150 Runs

We have these ScreenTapes available:

  • D1000 DNA ScreenTape
  • D5000 DNA ScreenTape
  • RNA ScreenTape

There are several other ScreenTapes that we may have available or can obtain; please inquire:

  • D1000 High Sensitivity DNA ScreenTape
  • D5000 High Sensitivity DNA ScreenTape
  • High Sensitivity RNA ScreenTape
  • Cell-free DNA ScreenTape
  • Genomic ScreenTape

We load 1-2 ul of each sample. Please provide at least 3 ul of samples arranged on strip tubes.

It is a standard process to heat denature RNA samples at 73°C before sample loading to remove secondary structures.

In deciding the mass of DNA to load, in general the broader your DNA species in size (e.g. NGS library), the more mass you should load within a kit’s specifications.

We will deliver data as a PDF file and will include the data file. You can download free TapeStation Analysis software to view XAD files at https://bit.ly/3nzGDgG. This is a link to third party online content. If you experience any issues accessing this content, please contact the Nevada Genomics Center.

Agilent Bioanalyzer chip specifications
Chip type Recommended loading mass Sizing range Electronic ladder available
D1000 ScreenTape 0.5 – 50 ng in 1 ul 35 – 1000 bp Yes
D5000 ScreenTape 0.5 – 50 ng in 1 ul 100 – 5000 bp No
RNA ScreenTape 25 – 500 ng in 1 ul N/A Yes
High Sensitivity D1000 ScreenTape 0.01 – 1 ng in 2 ul 35 – 1000 bp Yes
High Sensitivity D5000 ScreenTape 0.01 – 1 ng in 2 ul 100 – 5000 bp No
High Sensitivity RNA ScreenTape 1 – 25 ng in 2 ul N/A Yes
Genomic DNA ScreenTape 5 – 300 ng in 1 ul 200 – 60,000 bp No
Cell-free DNA ScreenTape 0.1 – 5 ng in 2 ul 50 – 800 bp Yes