The DNA Facility provides genomic or high throughput DNA sequencing services using the Roche Genome Sequencer FLX Systems (a.k.a. "The 454 Sequencer"). The DNA Facility has recently acquired the Applied Biosystems SOLiD v3 genome sequencer and will soon (late Summer 2009) be offering services based on its use.  Through a partnership with Iowa State University, UI investigators have equal access the the Illumina Genome Analyzer.

Roche Genome Sequencer FLX System:

The Genome Sequencer FLX System, using the Titanium chemistry, applies an innovative twist on pyrosequencing-based reagent technology that
enables massively parallel sequencing in high-density microwell plates permitting ~1,000,000 reads of ~400 nt in length from each run.

There are several possible types of experiments that can be done on this platform which has strengths in producing longer reads such as: 1) de-novo sequencing of an organism, 2) re-sequencing, 3) expression profiling (similar to a sage library), 5) exon capture re-sequencing (in conjunction with Nimblegen microarrays) and 6) deep sequencing (looking for rare somatic or population mutations). For more information on the 454 technology 454 Info .

Illumina Genome Analyzer II:
Information regarding Iowa State University genome sequencing service which features the short-read Illumina Genome Analyzer can be found at the ISU DNA Facility.  Through a partnership with the ISU DNA Facility, UI investigators enjoy ISU institutional priority access and pricing.

ABI SOLiDv3 Genome Sequencer:
The UI DNA facility has just recently acquired the ABI SOLiDv3 System.  The ABI SOLiDv3 is a short-read genome sequencer that uses a ligation-based sequencing chemistry with a novel 2-base encoding system to generate >20 GB and >400 million sequence tags per run.

We expect to start producing data on this system in mid-August.

Genome Sequencing Fees:
Fees vary by project type please inquire. A typical full plate run consisting of a library preparation, sample titration, and sequencing run yielding 100 MB of sequence data will cost approximately $9500.

Sample submission:
For a typical genome sequencing project, provide ~10 micrograms high molecular weight DNA in 50-100 microliters of Tris or TE. Please provide a photo of an agarose gel documenting your DNA sample quality.

Data Handling and Output:
The output from the run will be 1 to many (depending on the number of regions and ID tags used) FASTA files (i.e., sequence text files). We will deliver the results of your sequencing run, QC information on the sequencing run, along with the laboratory notes from the sample preparation to a password protected website where you will be able to download your data (18-22G typically).

We can also do an inital de-novo assembly using the newbler assembler where appropriate. This will assembly the run(s) based on homology between the reads but will probably not finish the assembly due to repetitive elements and regions that lack coverage. We can work with you to further analyze the data at additional cost. We have an 8 cpu 32G server with attached RAID to provide computing resources to help with additional annotation and analysis (BLAST, BLAT and alternative assembly algorithms).

Contacts:
For more detailed pricing or general information about the service contact: Kevin Knudtson(319) 335-7251

For information about sample preparation contact: Jennifer Bair or Einat Snir (319) 335-6736

For information about downstream bioinformatics support: Tom Bair (319) 335-6717