Service price list for external clients

Effective July 1, 2022

Prices are periodically evaluated during the year and are subject to change.

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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.

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 TapeStation 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 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)
2. Illumnia stranded mRNA Prep: 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

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:

1. Quantity of dsDNA or RNA must be determined using specific methods (e.g. Qubit)
2. For mRNA library generation: assessment of total RNA quality for each sample
3. Other information may be requested based on project specifics (e.g. cells per sample for single cell sequencing).

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
• High Sensitivity D1000 DNA ScreenTape
• RNA ScreenTape

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

• D5000 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.