Illumina Sequencing

The GC3F began offering Illumina sequencing services in the early days of next-generation DNA sequencing in 2008.  Since then, we have sequenced literally thousands of samples on multiple Illumina platforms.  We played a significant role in the development of the RAD-seq technique that was invented at UO, and are still happy to sequence “unconventional” libraries on our instruments.

The GC3F currently operates three Illumina DNA sequencers:

  • MiSeq
  • HiSeq 4000
  • NextSeq 500

(Note, our HiSeq 2500 has officially been retired from service!)

Prices for all run types are listed at the bottom of this page.



(as of 2/5/18)

If you'd like us to sequence a library that requires custom sequencing primers for any of the following reads:

Read 1, Read 2, Index 1 (i7), and/or Index 2 (i5)

We now ask that you provide these custom sequencing primers along with your library.

Please submit 30 µL of each custom sequencing primer (per lane) at a concentration of 100 µM. Please be sure to make a note in the "comments" section of your sequencing submission about which custom primers you are including.

Thanks for your cooperation!



Illumina MiSeq Sequencing 




We are excited to now offer sequencing on the Illumina MiSeq system! This is a benchtop instrument designed for lower-output sequencing applications such as amplicons (targeted resequencing), small genomes, miRNA & small RNA, and targeted gene expression profiling.

In addition to offering both single read (SR) and paired end (PE) read types, it has the longest read length available on any Illumina instrument and can be operated at 4 different modes to help you narrow in on the ideal configuration for your experiment:

  • v3 mode:  Up to 25M reads at max read length of 300bp
  • v2 mode:  Up to 15M reads at max read length of 250bp
  • Micro mode:  Up to 4M reads at max read length of 150bp
  • Nano mode:  Up to 1M reads at max read length of 250bp

Please submit 25 µL minimum volume of your MiSeq libraries at 4 nM minimum concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).  

For further details on sample submission, contact Doug Turnbull (


HiSeq 4000 Sequencing

Thanks to a generous donation to genomic research at UO, the GC3F is now offering Illumina HiSeq 4000 sequencing services.  The HiSeq 4000 utilizes the latest patterned flowcell technology from Illumina, yielding roughly 2x the per-lane read number (~400M reads) and data output as the older HiSeq 2500.  Compared to the HiSeq 2500, run times are dramatically faster, data quality is higher, and reagent prices are lower on the 4000.  We have established protocols for sequencing all popular library types on the new instrument (including RAD-seq!) and are accepting sample submissions now.

Please submit 25 µL minimum volume of your HiSeq libraries at 2 nM minimum concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable). 

Click here to submit a sample for sequencing!


NextSeq 500 Sequencing

The Illumina NextSeq 500 produces sequence data that is of similar quality to that of HiSeq 2500 High Output runs, at a similar cost. 

The NextSeq has two run modes: Medium and High Output. 

  • Medium output runs yield ~130M reads
  • High Output runs yield ~400M reads

One user-submitted library is loaded per run, so there is never any waiting for additional libraries to arrive in the facility to fill flowcells.  Read length options are slightly different, but NextSeq flowcells are 100% compatible with libraries generated for other Illumina sequencing instruments.  

Please submit 25 µL minimum volume of your NextSeq libraries at 2 nM minimum concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).

Click here to submit a sample for sequencing!



All libraries submitted for Illumina sequencing are quantified by qPCR, and fragment size distributions are measured using our AATI Fragment Analyzer.  There is no extra fee for these services (costs are included in the below sequencing rates).



To submit a sample for sequencing, please create an account on our website, and click "Submit Sample To Queue." For HiSeq 4000: If you are in a hurry to get your data, it is advantageous select multiple "allowed lengths." If you do so, we will put your sample on the next available run of an allowed read length rather than waiting for a run to fill up for one specific read length.

Please deliver samples to Maggie Weitzman in 288 Klamath Hall if you are an on-campus user.  For off campus users, please mail samples frozen on ice in a well-protected vessel to the following address:

        Genomics and Cell Characterization Core Facility
        Institute of Molecular Biology
        1318 Franklin Blvd, Room 272 Onyx Bridge
        University of Oregon
        Eugene, OR 97403-1229

Upon mailing your package, please send an email to so that we know to look for your shipment. 



* Users from UO, OSU, and OHSU are eligible for Internal pricing. All other users are considered External.

NOTE: MiSeq and NextSeq may have multiple run types at the same price. This is because some reagent kits allow us the flexibility to sequence at multiple read lengths. However, since these kits cannot be subdivided, we are unfortunately not able offer a lower price for reads lengths that are shorter than the maximum allowed for the kit.