Services

 

Illumina sequencing

We offer Illumina library preparation services using commercially available kits. We have three Illumina sequencing instruments: NextSeq 2000, NextSeq 550 and MiniSeq. Our sequencing output has a range of 8 million to 1.1 billion read/read pairs, or 2.4 to 330 gigabases. This is the equivalent of 0.6 to 110 human genome equivalents.

  • Illumina sequencing options
    Illumina NextSeq 550 sequencing options
    Instrument Kit type Cycles Sequencing kit cost Advertised reads/read pairs Advertised Gb Cost/Gb Cost/1M reads/read pairs Human equivalents
    NextSeq 550 Mid output 150 $1,120.05 1.30E+08 19.5 $57.44 $8.62 6.5
    NextSeq 550 Mid output 300 $1,805.00 1.30E+08 39 $46.28 $13.88 13
    NextSeq 550 High output 75 $1,536.15 4.00E+08 30 $51.21 $3.84 10
    NextSeq 550 High output 150 $2,945.00 4.00E+08 60 $49.08 $7.36 20
    NextSeq 550 High output 300 $4,716.75 4.00E+08 120 $39.31 $11.79 40
    Illumina NextSeq 2000 sequencing options
    Instrument Kit type Cycles Sequencing kit cost Advertised reads/read pairs Advertised Gb Cost/Gb Cost/1M reads/read pairs Human equivalents
    NextSeq 2000 P2 100 $1,420.00 4.00E+08 40 $35.50 $3.55 13.3
    NextSeq 2000 P2 200 $2,670.00 4.00E+08 80 $33.38 $6.68 26.7
    NextSeq 2000 P2 300 $3,540.00 4.00E+08 120 $29.50 $8.85 40
    NextSeq 2000 P3 50 $2,250.00 1.10E+09 55 $40.91 $2.05 18.3
    NextSeq 2000 P3 100 $3,250.00 1.10E+09 110 $29.55 $2.95 36.7
    NextSeq 2000 P3 200 $4,500.00 1.10E+09 220 $20.45 $4.09 73.3
    NextSeq 2000 P3 300 $6,000.00 1.10E+09 330 $18.18 $5.45 110
    Illumina MiniSeq sequencing options
    Instrument Kit type Cycles Sequencing kit cost Advertised reads/read pairs Advertised Gb Cost/Gb Cost/1M reads/read pairs Human equivalents
    MiniSeq Rapid high output 100 $1,050.00 2.00E+07 2 $525.00 $52.50 0.7
    MiniSeq High output 75 $855.95 2.50E+07 1.88 $456.51 $34.24 0.6
    MiniSeq High output 150 $1,003.20 2.50E+07 3.75 $267.52 $40.13 1.3
    MiniSeq High output 300 $1,604.55 2.50E+07 7.5 $213.94 $64.18 2.5
    MiniSeq Mid output 300 $572.85 8.00E+06 2.4 $238.69 $71.61 0.8

    * Yields are as advertised by Illumina. Results will vary.

  • Illumina sample submission guidelines

    Contact the Nevada Genomics Center to begin an Illumina sequencing project.


 

Sanger sequencing

The Nevada Genomics Center operates a 3730 DNA Analyzer for Sanger sequencing. All of our runs include an internal plasmid control to aid in quality control.

Samples submitted by 2 p.m. Monday-Thursday are guaranteed to have data returned the following day.

  • Sanger sequencing sample submission guidelines
    • Submit requests with our dnaTools LIMs
    • Email phartley@unr.edu with any questions related to using dnaTools.
    • Follow the guidelines for the optimal amount of template and primer for Sanger sequencing..
    • We request a minimum volume of 5uL; if your sample is less than 5uL please add water to bring the submitted sample up to 5uL. The maximum volume we accept is 25uL, so if your template DNA is too dilute please concentrate it.
    • Submitted samples should be in water. EDTA will inhibit the Sanger reaction.
    • For PCR amplicons:
      • Ensure only one PCR product is present (visualize with a gel).
      • PCR reactions must be cleaned up prior to sequencing using routine cleanup kits. We offer PCR cleanup services.
    • Use a dsDNA-specific quantification method (e.g. Qubit, picogreen) to quantify your templates. We offer quantification services.
    • View the list of common sequencing primers provided by Nevada Genomics Center.
    • How to submit your samples:
      • Using 8-well strip tubes:
        • Label each tube with the sample number (1, 2, 3, …).
        • Write the order number on the side of the first tube of the strip.
      • Using 96-well plates:
        • Submit a maximum of 96 samples per order if you are using plates.
        • Order samples down columns. Sample 1 is A1, sample 2 is B1, etc.
        • Write the order number on the plate.
  • Downloading your Sanger sequencing data

    Sequencing data are provided in text and ab1 format for download via the dnaTools server.


 

Fragment analysis/genotyping/DNA fingerprinting

Fragment analysis can be performed using microsatellite or RFLP techniques. Samples are run on the 3730 DNA Analyzer, which is equipped with filters compatible with 6-FAM, VIC, NED, PET and LIZ (for size standards).

We can run plates provided as-is, or prepare your samples by diluting (if necessary) and adding size standard (LIZ 500).

We will determine the best dilution for your samples if necessary for a nominal fee.

  • Fragment analysis/genotyping sample submission guidelines
    • Submit requests with our dnaTools LIMs.
    • Email phartley@unr.edu with any questions related to using dnaTools.
    • Ensure that your sample prep process (PCR) is working optimally and robustly. We recommend being able to dilute PCRs by at least 100-fold for optimal capillary runs.
    • How to submit your samples:
      • Using 8-well strip tubes:
        • Label each tube with the sample number (1, 2, 3,…).
        • Write the order number on the side of the first tube of the strip.
      • Using 96-well plates:
        • Submit a maximum of 96 samples per order if you are using plates.
        • Order samples down columns. Sample 1 is A1, sample 2 is B1, etc.
        • Write the order number on the plate.
  • Downloading Your Fragment Analysis/Genotyping Data

    Data are provided in fsa format for download via the dnaTools server.


 

PCR cleanup

We offer PCR cleanup for Sanger sequencing services. Your samples will be quantified and an appropriate amount is used in an enzymatic reaction that degrades remaining PCR primers and dephosphorylates remaining dNTPs. This treated sample can then be used directly in Sanger sequencing.

  • Sample submission guidelines for PCR cleanup

    How to submit your samples:

    • Using 8-well strip tubes:
      • Label each tube with the sample number (1, 2, 3,…).
      • Write the order number on the side of the first tube of the strip.
    • Using 96-well plates:
      • Submit a maximum of 96 samples per order if you are using plates.
      • Order samples down columns. Sample 1 is A1, sample 2 is B1, etc.
      • Write the order number on the plate.

 

Quantification services

We use quantification methods specific for dsDNA or RNA.

Up to 48 samples will be quantified with a Qubit fluorometer.

A plate-based assay will be used to quantify 48 or more samples. Standards are measured in triplicate and you can request multiple measurements of your samples.

  • Sample submission guidelines for quantification

    We must be able to pipet a minimum of 2 ul of your samples; provide 3 ul.

    How to submit your samples:

    • Using 8-well strip tubes:
      • Label each tube with the sample number (1, 2, 3,…).
      • Write the order number on the side of the first tube of the strip.
    • Using 96-well plates:
      • Submit a maximum of 96 samples per order if you are using plates.
      • Order samples down columns. Sample 1 is A1, sample 2 is B1, etc.
      • Write the order number on the plate.

    You will receive a spreadsheet listing the concentration of your samples. If you requested a plate-based assay for quantification, the data, including standard curve and subsequent calculations, will be included.


 

Agilent TapeStation 4150 services

The Agilent TapeStation 4150 can be used to determine the size range of DNA or RNA samples. RIN numbers are reported for RNA samples. We are currently offering three types of ScreenTapes as part of our regular services. Please contact us if you are interested in the High Sensitivity versions of the DNA & RNA ScreenTapes, as well as cell-free and genomic (up to 60 kb) DNA ScreenTapes.

TapeStation D1000

Samples should be 0.1 to 50 ng/ul.  The dynamic size range is 35 to 1,000 bp.

TapeStation D5000

Samples should be 0.1 to 50 ng/ul.  The dynamic size range is 100 to 5,000 bp.

TapeStation RNA

Samples should be 25 to 500 ng/ul.

  • Sample submission guidelines for Agilent

    Runs require 1-2 uL of sample, but please submit a minimum 3uL aliquot so that we may accurately remove a 1-2 uL aliquot. We can process any number of samples. Please submit samples in strip tubes.

  • Data

    Both a data file and PDF documents with the results are emailed to you. Data files can be viewed with TapeStation software, which can be downloaded from Agilent.


 

QuantStudio 3 services

We have a QuantStudio 3 that can be used with 0.2 ml PCR plates.