Illumina Sequencing





NEWS 9/9/2021:

Why are we posting this news?

You may have noticed a new option to select “NovaSeq 6000” within the Illumina Sequencing queue. However, this feature is actually still under construction and unfortunately does not include any samples that were submitted in iLab prior to deploying this feature. Because of this, we are still manually curating the table below so that we can display all samples from both before AND after deploying this feature. THEREFORE YOU SHOULD REFER ONLY TO THIS MANUALLY CURATED TABLE, and we advise you to ignore the “NovaSeq” option that's now showing up the queue until feature gets fully built out (at which point this manually curated queue will be taken down and the "queue" link in the left panel menu will direct you to the fully built queue)! Thanks for your patience!

Color code legend:

Sample not yet received / Library prep in progress
Sample received, QC / Quantification / Pooling in progress
Ready to load on the NovaSeq
Currently sequencing / data processing


Sample ID

Output Mode

Run Type

GC3F-CM-5008 SP SR 100
GC3F-KK-4694 SP SR 100
GC3F-PP-4824 SP SR 100
GC3F-MM-4954 SP SR 100
GC3F-BB-5073 SP SR 100
GC3F-SN-5010 SP SR 100
GC3F-ES-5109 SP SR 100
GC3F-ES-5126 SP SR 118
GC3F-ES-5127 SP SR 118
GC3F-MM-5094 SP SR 100
GC3F-DG-4983 SP PE 150
GC3F-CA-4686 SP PE 150
GC3F-PE-5079 S1 SR 100
GC3F-JD-5093 S1 SR 100
GC3F-TW-5072 S4 PE 150
GC3F-JS-4663 S4 PE 150
GC3F-JS-4666 S4 PE 150
GC3F-JS-4664 S4 PE 150
GC3F-JS-4665 S4 PE 150
GC3F-AB-5108 S4 PE 150
GC3F-AB-5107 S4 PE 150
GC3F-VM-5128 S4 PE 150
GC3F-IS-4715 S4 PE 150
GC3F-IS-4715 S4 PE 150
GC3F-SR-4843 S4 PE 150
GC3F-AE-4981 S4 PE 150




We are currently operating according to policies described in our approved Stage 1 Recovery Plan.

A summary of these policies is posted up around the core, as well as HERE.



CLICK HERE to get answers to our most frequently asked COVID-19 operational status questions.



We have had an increasing number of requests for the retrieval of old sequencing data from our archive. While we are always happy to help whenever we can, a couple of issues have arisen surrounding this. CLICK HERE to review our new policy on data retention & retrieval.



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
  • NovaSeq 6000
  • NextSeq 500

(Note, our HiSeq 4000 service will end on June 1, 2021)

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




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 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 NovaSeq 6000 Sequencing 

 Thanks to a generous award from the Murdock Charitable Trust, GC3F is now offering Illumina sequencing services on a NovaSeq 6000 sequencer. The NovaSeq will be taking the place of our workhorse HiSeq 4000, and offerings the following advantages over the older platform:

  • Multiple output modes from 400M up to 2500M read pairs per lane
  • Lower cost per Gbp than HiSeq 4000, even in the lowest NovaSeq output mode (SP)
  • Lowest cost per Gbp of any available sequencing platform in high output (S4) mode
  • Fewer lanes per flowcell = less lead time waiting for lane submissions from other users needed to launch runs
  • Full compatibility with all Illumina library types


Log in to iLab to submit a sample to run on the NovaSeq!

Pricing info for single-lane NovaSeq sequencing

Run Type

Internal Rate

External Rate

Run Configurations

Read Pairs per lane**

S4 300 Cycle $4500 $5625 PE 2x150 2-2.5 billion+
S4 35 Cycle $3300 $4163 SR 53*, PE 2x32* 2-2.5 billion+
S1 300 Cycle $3300 $4163 PE 2x150 650-800 million+
S1 100 Cycle $2490 $3113 SR 118*, PE 2x59* 10X scRNA 650-800 million+
SP 500 Cycle $2700 $3375 PE 2x250 325-400 million+
SP 300 Cycle $1980 $2475 PE 2x150 325-400 million+
SP 100 Cycle $1440 $1800 SR 118*, PE 2x59* 10X scRNA 325-400 million+

*All NovaSeq kits contain sufficient reagent to sequence an additional 38nt beyond the specified cycle number (SP 100 cycle kits contain reagents for 138 cycles, S4 35 cycle kits contain reagnets for 73 cycles, etc). These can be used for 10X cell barcodes, long dual index reads, or extended read length for the library inserts

**These are the official Illumina output specs and are conservative. Real world performance will often exceed these read numbers



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 2-20 nM 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 MiSeq sequencing request! (Note, you will need to register for an iLab account.)



HiSeq 4000 Sequencing

The HiSeq 4000 has been replaced by the NovaSeq 6000 in our core. Please contact us if HiSeq 4000 data is essential to complete existing projects ! 

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. The spec for read output is 312.5M reads per lane, but we routinely obtain higher than this and typically expect ~350M reads for most libraries. 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 2-20 nM concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable). 



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 2-20 nM 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 NextSeq 500 sequencing request! (Note, you will need to register for an iLab account.)




All single tubes 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).

However, if you are submitting mutliple tubes for sequencing and wish for us to individually QC and multiplex them prior to sequencing on a single lane, that is considered a separate Sample Prep request and costs an additional $12.50 per sample (on top of the standard sequencing price) Please contact with questions!




To submit a sample for sequencing, please register for an iLab account and then click "Request Services" from the top menu bar in iLab. It is important that your request has been submitted in iLab before you provide the physical samples to us!

NOTE: 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 submit 25 µL minimum volume per sample at 2-20 nM concentration in Qiagen EB buffer (10 mM Tris pH 8.5) with 0.1% tween 20 (other standard DNA storage buffers are also acceptable).

Please deliver samples to Jeff Bishop 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:

University of Oregon/GC3F
1318 Franklin Blvd
Room 273 Onyx Bridge
Eugene, OR 97403

NOTE: Please ensure that your package will arrive for delivery at UO only on Mon-Thurs. Due to campus restrictions during the COVID-19 pandemic, UO cannot accept deliveries on Fri-Sun.




* 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.




We do our best to give an accurate estimate of turnaround time when service requests are submitted. These estimates are not guarantees and occasionally change due to unforeseen circumstances (instrument maintenance/repairs, staff sick leave, etc.). Please let us know if you have a hard deadline on project completion when you submit your service request and we will take measures to ensure that we either meet that deadline or inform you ASAP if circumstances beyond our control will cause us to miss it. Thanks!