Services

 

Illumina Sequencing

We offer Illumina library preparation services using commercially available kits. Our NextSeq 500 has several options for sequencing yield, ranging from 18-120 Gb (6 to 40 human genome equivalents).

We use quantitative PCR to aid in pooling samples. Pooled libraries are checked one additional time by qPCR to ensure optimal clustering.

Sequencing run data are transferred to clients via the BaseSpace transfer ownership function.

Funding for Illumina NextSeq 500 was generously provided by Dr. Michael J.M. Hitchcock


 

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.

For samples received Monday-Thursday by 10 a.m., you will be able to download your data the next day in the afternoon. Samples received after 10 a.m. Thursday or on Friday will be processed the following Monday with data available Tuesday afternoon.

  • 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 (typically 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 use commercially available kits for PCR cleanup.

  • 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 16 samples will be quantified with a Qubit fluorometer.

A plate-based assay will be used to quantify 16 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 BioAnalyzer services

The Agilent 2100 BioAnalyzer system is a chip-based microfluidics-based platform for sizing, quantitation, and quality analysis of both dsDNA and RNA samples.

Agilent 6000 Nano RNA

RNA samples run with this kit should be 25 to 500ng/uL. The chip capacity is 12 samples.

Agilent 7500 DNA

Size range is 100-7500 bp. Samples should be 0.1 to 50ng/uL. The chip capacity is 12 samples.

Agilent High Sensitivity DNA

Size range is 50-7500 bp. Samples should be 5-500pg/uL. The chip capacity is 11 samples.

  • Sample submission guidelines for Agilent

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

    For RNA samples originating from insects, it may be advisable to skip the routine heat denaturation step prior to running a RNA chip. Discuss this with NGC staff when submitting these types of samples.

  • Data

    Results are emailed to you in PDF format at a minimum. You can request the raw data files that can be viewed with Bioanalyzer 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.