Illumina NextSeq 500

The UAGC offers a variety of Illumina NextSeq500 supported applications including Shotgun/de novo sequencing, RNAseq, Exome sequencing, Small RNA profiling as well as other custom NGS pipelines.

Sample Input

DNA or RNA from a variety of sample types can be run on Illumina NextSeq 500 including cells, tissue, and blood. We also offer DNA or RNA extraction for library prep.

Applications include:

  •  Whole Genome Sequencing (Shotgun/de novo)
  •  RNASeq (transcriptome sequencing)
  •  Exome Sequencing
  •  Mate Pair Sequencing (3kb, 5kb, 10kb)
  •  miRNA profiling
  •  CHiPseq
  •  Metagenome Analysis
  •  Other supported and custom protocols (please inquire)
Expected Results

Expected Results:

  • Read lengths - 1x75, 2x75, 2x150
  • Average data output 
    • 1x75 High Output: 25Gb - 30Gb
    • 2x75 Mid Output: 16.25Gb - 19.5Gb
    • 2x75 High Output: 50Gb - 60Gb
    • 2x150 Mid Output: 32.5Gb - 39Gb
    • 2x150 High Output: 100Gb - 120Gb

Data Delivery:  Data may be accessed using the UofA HPC or downloaded to your machine via Cyberduck. See the following user guides for detailed instructions: Cyberduck User Guide OR  HPC-iRODS User Guide

  • Untrimmed reads 
  • Reads trimmed by Trimmomatic

    • Organized into paired reads and reads whose pair was not retained due to quality trimming

    • In addition to trimming Illumina adapter sequence, trimmomatic parameters used are: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 

  • Fastqc_out folder containing zipped quality reports

Inquire at for run prices and quote.

Sample Preparation Details

DNA sample requirements (if not submitting tissue, cells, ect. for extraction):

  • 100ng - 3ug total DNA required (shotgun/de novo and Exome sequencing)
  • 3µg - 10µg total DNA for 3kb and 5kb mate pair libraries
  • 10+ ug total DNA for 10kb mate pair libraries
  • DNA sample should be suspended in LowTE or water
  • DNA should not be degraded
  • DNA should have an OD 260/280 ratio ≥ 1.8
  • DNA must be double stranded
  • DNA should not be the result of whole genome amplification (or other process that can compromise accurate representation)
  • DNA should contain no particulate matter

RNA sample requirements:

  • 100ng - 3ug total RNA required
  • RNA should not be degraded
  • RNA should be resuspended in RNAase free water or RNA preservative

​How to Get Started with your Sample Submission:

  • Complete the Request a Quote form and we will contact you to discuss your project workflow. 

Quality Control of Samples-Every sample received for sequencing will go through a set of quality control checks before it can be processed. Customers may be asked for more DNA/RNA if their sample fails either of the following check points:

  • Qubit to verify the quantity of starting material
  • Fragment Analyzer to check the material quality

Cluster Generation

Cluster generation requires 10nM post library construction concentration.

Sequencing Chemistry

The UAGC uses Illumina NextSeq 2-channel SBS chemistry.​

Library preparation/construction

UAGC uses a variety of DNA/RNA construction kits. 

*Note- Per Illumina recommendations we can not run libraries that are more than 6 months old. Therefore, your library material will be disposed of 6 months after they are built in accordance with our SOPs.

Data Analysis

Supplementary data analysis will incur additional labor rates. Please contact Genome Analytic Services to discuss further data analysis needs.


Academic(UofA): $ Varies | Industry: $ Varies | Unit: Flow Cell

Turnaround Time

Average turnaround time will vary dependent upon application and sample input. 

Average data turnaround time for most NGS projects is approximately 4-6 weeks. 

The UAGC operates on a first come, first serve entry into sample queue. 

Additional Information

If there is a specific application you are interested in on the NextSeq500 but do not see listed here, please contact us to see if we can accommodate your needs!

University customers: We are located in the Keating Building, room 124. Samples may be left in the freezer at the north entrance to our lab. Samples should be clearly labeled "Illumina" along with your contact information and billing account.

External customers: Samples should be shipped pre-frozen and preferably on dry ice (although regular ice packs work well enough for overnight shipping). Sample tubes should be sealed with parafilm.

Shipping address:
University of Arizona Genetics Core
Attn: NGS Team
1657 E. Helen Street
Keating Building, Rm 124
Tucson, AZ 85721

  • The NextSeq500 offers robust sequencing capabilities at a lower cost-per-base.

    Stephen Stern

For this service, please contact