Illumina MiSeq

The UAGC offers Illumina MiSeq supported applications including DNASeq, RNAseq, targeted gene sequencing, Metagenomics (16S/custom) small genome sequencing amplicon sequencing and other NGS pipelines.

Sample Input

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

Applications include:

  •  Small Genome Sequencing (Shotgun/de novo)
  •  RNASeq (transcriptome sequencing/expression analysis)
  •  Cancer Genomics (RUO)
  •  Methylation Analysis
  •  miRNA profiling
  •  CHiPseq
  •  Metagenome Analysis (16S/custom)
  •  Other supported and custom protocols (please inquire)
Expected Results

Expected Results: Select from Version 2 (v2) or Version 3 (v3)


  • Read length: 1x36SR, 1x50SR, 2x25PE, 2x150PE, 2x250PE
  • Average data output: 540Mb (1x36SR), 750Mb (1x50SR, 2x25PE), 4.5Gb (2x150PE), 7.5Gb (2x250PE)


  • Read length: 2x75PE, 2x300PE
  • Average data output: 3.3Gb (2x75PE), 13.2Gb (2x300PE)

Data Delivery: All data is delivered via Cyberduck. See the following user guides for detailed instructions: Cyberduck User Guide

  • Fastq format reads as trimmed by MiSeq Workflow
  • Any ancillary reports produced by the MiSeq Workflow

Click on the 'Details' tab above for rate information and how to submit samples.

Sample Preparation Details

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

  • 3ug total DNA required (shotgun/de novo and Exome sequencing)
  • 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 contain no particulate matter

RNA sample requirements:

  • 200ng-4ug total RNA required depending on application
  • RNA should not be degraded
  • RNA should be resuspended in RNAase free water and kept at -80C until delivery to UAGC

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:

  • Pico/RiboGreen Assay to verify the quantity of starting material
  • Bioanalyzer DNA/RNAchip to check the material quality

Cluster Generation-
Cluster generation run between 10-12uM post library construction concentration

Sequencing Chemistry-
The UAGC uses TruSeq SBS Chemistry.

Library preparation/construction-
UAGC uses DNA/RNA TruSeq library construction kits
Maximum 12 samples multiplexed per lane (UAGC provides MID tagging)

*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 approx 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 Illumina MiSeq 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: Illumina NGS
1657 E. Helen Street
Keating Building, Rm 124
Tucson, AZ 85721

  • Next Generation Sequencing on the Illumina MiSeq offers researchers affordable sequencing options while maintaining a great dept of coverage.

    Jon Galina Mehlman

For this service, please contact