Illumina Sequencing

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 two DNA sequencers, an Illumina HiSeq 4000 and a NextSeq 500. (Note, our HiSeq 2500 has officially been retired from service!)

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 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.

Click here to submit a sample for sequencing!

HiSeq 4000 Single Lane Pricing
Run Type Internal rate (UO, OSU, PSU, OHSU) External Rate
Single Read 75 $770 $1193
Single Read 100 $912 $1411
Single Read 150 $1053 $1630
Paired End 75 $1319 $2040
Paired End 100 $1459 $2258
Paired End 150 $1741 $2695

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 ~130 million reads.  High Output runs yield ~400 million. 

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.  

NextSeq 500 Run Pricing:

Run Type Internal Rate External Rate
Medium Output (130M reads) Single End 150 $1,109 $1,876
Medium Output (130M reads) Paired End 75 $1,109 $1,876
Medium Output (130M reads) Paired End 150 $1,779 $3,010
High Output (400M reads) Single End 75 $1,488 $2,517
High Output (400M reads) Single End 150 $2,847 $4,817
High Output (400M reads) Paired End 37 $1,488 $2,517
High Output (400M reads) Paired End 75 $2,847 $4,817
High Output (400M reads) Paired End 150 $4,556 $7,708

Included Library QC and Quantification

All libraries submitted for either HiSeq or NextSeq 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 standard sequencing rates).

Sample Submission

To submit a sample for sequencing, please create an account on our website, and click "Submit Sample To Queue". 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.

Samples must be diluted to a concentration between 2 and 20 nanomolar in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).  Please submit at least 25 microliters of your sample.

*** NEW SAMPLE SHIPPING ADDRESS, as of 11/15/16 ***

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.