DNA Sequencing Facility: Illumina (Solexa) Sequencing

The DNA Sequencing Facility maintains an Illumina Genome Analyzer IIx (GAIIx) sequencers and two Illumina HiSeq 2000 systems. Illumina sequencing is based upon Solexa sequencing-by-synthesis technology. Illumina libraries are run on a flowcell which contains 8 individual lanes.  Customer samples can be run each in a single lane, over multiple lanes, or can be placed together in a single lane using DNA barcodes, depending on the amount of sequencing needed.

System Overview

Illumina GAIIx:

• Read Length: 36, 75 or 100 bp, single read or paired end
• Run time: 2-12 days
• Data generation per lane: 12-30 million fragments sequenced in parallel; 1.5-3.5 Gbases data output.
• Ideal for: ChIP-seq, smallRNA-seq, small genome resequencing and targeted capture

Illumina HiSeq 2000:

• Read length: 50 or 100 bp, single read or paired end
• Run time: 3-12 days
• Data generation per lane: 50-150 million fragments sequenced in parallel; 3 - 30 Gbases data output.
• Ideal for: RNA-Seq, de novo small genome sequencing, large genome resequencing and targeted sequencing

**Pricing listed above will be effective starting October 1, 2011. 75 bp HiSeq runs will be phased out at this time because of low demand.**

EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 50.5% surcharge for all labor provided; prices are as listed above.  This surcharge is subject to change.

Illumina pricing is broken into two components: library preparation and run cost.  Library preparation is charged on a per sample basis and varies by type.  Run charges are based on the length of the sequencing run and whether it is single direction or paired end.  Prices are subject to change due to increasing reagent costs.

Scheduling and Sample Submission

Please contact nextgen-seq@biotech.wisc.edu for scheduling information. All projects must be discussed with a project manager prior to submitting samples. No projects will be scheduled until samples and sample submission forms have been dropped off to DNA Sequencing personnel in room 1250 Biotech Center.

•  Illumina Submission Form

Policy Statement

All data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequence Facility are intended for research purposes only. They are not intended nor certified for diagnostic or clinical use.

Every effort is made to provide our users with data that meets Illumina performance specifications for both the GAIIx and HiSeq2000 in a timely fashion. Turnaround time for Illumina sequencing is typically 1-2 months due to the length of each run and the limited number of libraries that can be placed onto each flowcell.  For more information, please review our Illumina sequencing policy prior to submitting samples.

Bioinformatics

Support is available for projects that are run at UWBC facilities, and is provided for a fee by the UWBC Bioinformatics Resource Center (formerly AGAR).  Terminals and software are available in our computer lab for clients of UWBC facilities who are internal to UW-Madison or the University of Wisconsin System who need to perform further analysis but lack the necessary hardware and software. Information on the quality reports distributed with your data is a available here.