Service price list for NSHE institutions

Effective 7/01/2019; Fiscal year is 7/1/2019-6/30/2020

The Nevada Genomics Center operates on a recharge basis in that all costs associated with operating the center must be recaptured. Prices will be evaluated at least 1-2 times during FY20 for any adjustments – up or down – required. The volume of services being ordered is expected to be the major determinant for any required changes in pricing during FY20.

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 NSHE-affiliated institutions
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 $5.25 / 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; ($8 if ≤ 8 samples)
Fragment analysis run: run prepared sample on capillary gel $3.00 / sample
Fragment analysis dilution optimization: client prepares plate ready to load directly onto capillary gel. Standards cannot be included in samples. Client interprets data. $12.50 / half plate; $25.00 / full plate
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. $85.00 / panel
Illumina NextSeq 500 services and pricing ( see two workflow examples for Illumina sequencing)
Service Rates for NSHE-affiliated institutions
Start NextSeq 500 sequencing run $70.00 / run
Validate pooled library concentration by qPCR $44.75 / pool
Library pooling service (already included in library preps done by NGC) $31.75 + $8.25 / 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) $300.00 + $50.00 / sample
Illumina TruSeq Nano PCR-Free (1-2 ug input gDNA) $300.00 + $50.00 / sample
Illumina TruSeq mRNA stranded (100 ng-1 ug input total RNA) $370.00 + $60.00 / sample
Illumina Nextera XT (1 ng input gDNA) $240.00 + $50.00 / 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 NextSeq 500 v2.5 sequencing kits services and pricing (5% discount + 4% S&H). Prices are subject to change but should be valid thru the end of 2019. Yield and number of read pairs are as advertised by Illumina. We recharge your provided Worktag when kit is received.
Service Rates for NSHE-affiliated institutions
Mid output v2.5, 150 cycles (18 Gb, 120M read pairs) $1,131.26
Mid output v2.5, 300 cycles (36 Gb, 120M read pairs) $1,822.86
High output v2.5, 75 cycles (30 Gb, 400M reads) $1,551.16
High output v2.5, 150 cycles (60 Gb, 400M read pairs) $2,973.88
High output v2.5, 300 cycles (120 Gb, 400M read pairs) $4,762.16
Agilent Bioanalyzer 2100 services and pricing ( see details for other chip types)
Service Rates for NSHE-affiliated institutions
High Sensitivity DNA (up to 11 samples) $76.50
DNA 7500 (up to 12 samples) $51.00
RNA Nano (up to 12 samples) $58.00
DNA quantification services and pricing
Service Rates for NSHE-affiliated institutions
Qubit HS DNA (max 100 ng, up to 16 samples) $2.00 / sample
dsDNA-specific plate assay (max 200 ng, up to 72 samples) $12.75; + $1.50 / sample
RNA quantification services and pricing
Service Rates for NSHE-affiliated institutions
Qubit HS RNA (max 100 ng, up to 16 samples) $2.00 / sample
RNA-specific plate assay (max 500 ng, up to 72 samples) $13.00; + $1.50 / sample
PCR cleanup service and QuantStudio 3 usage pricing
Service Rates for NSHE-affiliated institutions
PCR cleanup $4.00 / 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.

mRNA-seq of 12 mammalian samples
Item Units Total cost
Base rate for mRNA library prep 1 $370.00
Prepare 12 samples (includes pooling) 12 $720.00
Obtain sample size distributions with Agilent DNA 7500 1 $51.00
Confirm concentration of pooled samples 1 $44.75
Purchase high output 150 cycle (2x75) kit (60 Gb) 1 $2,973.88
Start sequencing run 1 $70.00
Total cost for all items 17 $4,229.63
Sequencing of 16 metagenomic samples
Item Units Total cost
Base rate for Nextera XT library prep 1 $240.00
Prepare 16 samples (includes pooling) 16 $784.00
Obtain sample size distributions with Agilent DNA HS 2 $153.00
Confirm concentration of pooled samples 1 $44.75
Purchase mid output 150 cycle (2x75) kit (18 Gb) 1 $1,131.26
Start sequencing run 1 $70.00
Total cost for all items 22 $2,423.01

 


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

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.

We’ll be observing whether ordering volume increases during FY20 and eventually may stock popular items on-site so you can get them on the same day.

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 10 a.m. Mon-Thurs for data delivery the following afternoon. Samples received after 10 a.m. Thursdays will be processed on Monday for data delivery Tuesday.

If we see sufficient increase in sequencing requests, we can strive towards offering same- day sequencing.

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 + internal size standard master mix. Heat denaturation will be performed on request.

You can submit fewer than 8 samples, but we have to charge the 8 sample minimum because of the method used to prepare the size standard + formamide 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.

We provide plates for free if you prepare your own samples. Please contact us and we can give you an appropriate number of plates for your throughput.

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 3:00 PM 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 (PCR, etc) 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. The cost is $12.50 for a half plate (the 6 odd- numbered columns) and $25.00 for a full plate.

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. The cost is $85.00.

Illumina – start NextSeq 500 sequencing run

This is the cost of starting any type of NextSeq 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.

We recommend qPCR quantification of a pooled 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.

Illumina – validate pooled library concentration

We will validate the effective concentration of your library by qPCR using a commercially available Illumina quantification kit. 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 same qPCR run a library that was previously observed to cluster well on a flow cell using our NextSeq; this helps us feel confident about how your library pool will perform when loaded onto our NextSeq.

Library Pooling Service

This is included in the price of our library prep services. We will use qPCR and a commercially available Illumina library 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.

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 Nextera XT: construct a library from most types of DNA using tagmentation
    • 1 ng input
    • Illumina TruSeq Stranded mRNA: construct a polyA enriched mRNA library
    • 100 ng – 1 ug total RNA input (we prefer no more than 500 ng to avoid overamplification)

All sample prep service prices include:

  • DNA 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.

If you request library prep, we may have to schedule a date (i.e. service is not immediate) to begin prep, depending on our workload and queue.

PCR cleanup

Typically done for cleanup of PCR products prior to Sanger sequencing. Does not include DNA quantification required prior to Sanger sequencing.

Large numbers of samples are cleaned up with a Zymo-96 plate-based kit. Smaller numbers of samples are cleaned up with a microfuge tube-based Qiagen PCR cleanup kit.

DNA quantification

1-16 Samples (with Qubit dsDNA HS)
8-72 Samples (plate-based)
Standards for plate-based assay

We use dyes specific for dsDNA binding for DNA quantification. By default, we will assay up to 16 samples with the Qubit. Any more than 16, 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

1-16 Samples (with Qubit HS kit)
8-72 Samples (plate-based)
Standards for plate-based assay

We use dyes specific for RNA binding for RNA quantification. By default, we’ll assay up to 16 samples with the Qubit. Any more than 16, 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

High Sensitivity DNA Chip
DNA 7500 DNA Chip
RNA Nano Chip

Agilent produces several other chip types (e.g. DNA 1000, RNA Pico, small RNA), but we do not stock these due to low usage. If you would like to use a chip type not listed here, please contact the NGC to discuss; most likely we would request you purchase a kit for your own use and a fee would be applied for setting up Bioanalyzer runs.

We load 1 ul of each sample. Please provide samples arranged on strip tubes. For DNA chips, 2 ul is the minimum to provide. For RNA chips, provide at least 5 ul as we will heat denature this amount first (but see below). If you also need us to quantify your samples, be sure to include an extra 3 ul of sample.

It is a standard process to heat denature RNA samples at 70°C before sample loading to remove secondary structures. For insect RNA samples, it may be best to skip the heat denaturation step to obtain more correct RNA quality results – see this paper: bit.ly/31CWaSm. This is a link to third party online content. If you experience any issues accessing this content, please contact the Nevada Genomics Center.

Tell us if you do not want us to heat denature RNA.

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 XAD data file. You can download free software to view XAD files at bit.ly/2Ioi58x. 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
High Sensitivity (broad DNA size, e.g. NGS libraries) 1 – 5 ng 50 bp – 7000 bp
High Sensitivity (amplicons) 5 – 500 pg 50 bp – 7000 bp
DNA 7500 0.5 – 50 ng 25 bp – 7000 bp
RNA Nano 25 – 500 ng 25 nt – 6000 nt