biogem

Sequencing Services

Services

BIOGEM is fully equipped to process sequencing runs on Illumina's 1G Analyzer once the sequencing libraries have been provided to us by the investigator.

Step to perform an Illumina 1G sequencing run at BIOGEM:

Decide which sequencing application and read length best suits your needs.The available options can be found at www.illumina.com/sequencing/.

For further questions please contact:

Elizabeth Boyer
Field Applications Scientist
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121-1975
Tel: 619-813-9846
E-mail: eboyer@illumina.com

Purchase the appropriate library prep kit, cluster generation kit (for GA2), and sequencing kit (for GA2). If you intend on using multiple sequencing primers you need to order an additional hybridization manifold.

For help with ordering please contact:

Chad D. Geringer
Regional Account Manager-Arizona, San Diego, Mexico, Central & South America
Illumina, Inc
9885 Towne Centre Drive
San Diego, CA 92121-1975
Tel (cell): 858-201-9695
E-mail: cgeringer@Illumina.com
or Illumina's technichal support: 800-809-4566

Please ship all reagents to your lab. The sequencing reagents, along with your libraries, should be dropped off at BIOGEM just prior to your scheduled run. Coordinate a drop-off day/time with James Sprague .

Prepare your libraries. Accurate library quantitation is key to obtaining optimal sequencing data output: please follow Illumina's protocol closely for this. For first-time users we also recommend getting additional help from Elizabeth Boyer and/or Illumina's technical support: (800) 809-4566.
Fill out the Online Form
Coordinate library & reagent drop-off with James Sprague . Libraries must be provided at a concentration of 10nM (5ul minimum).

The sequencing takes place on a flowcell, which has 8 lanes. This allows for 7 samples plus a control sample (PhiX, which we provide) per run. The first time a sample is used Illumina recommends running a concentration range to optimize the data output. This requires 3 lanes per sample. We have found this extremely important when running libraries from a first-time sequencing user.

You may decide to run less than 7 lanes, however turnaround time will then be dependant on when we receive other samples that would then fill up the remaining lanes. This is likely to take a while because most labs ask us to run full flowcells priority is given to labs running full flowcells. For the fastest turnaround time, we recommend you submit samples in groups of 7. Or if you are doing a concentration range on one or more of your samples, then we recommend you provide us with the number of samples it would take to fill up the 7 lanes of a flowcell. If you do decide to run less than a full flowcell, do not purchase the cluster generation or sequencing kit. BIOGEM will purchase both kits & then include a reagent charge on your bill, according to how many lanes you are using.

Once the raw sequencing data has been generated it will be run through Illumina's Pipeline v1.4 by James Sprague. Please let him know in advance if you intend on providing him with a custom config file. The sequence text files, along with the raw tiff images, will be copied to an external hard drive for you to borrow and copy to your own computer. You will receive an e-mail when the drive is ready for pick-up. Please be sure to sign the logout sheet when you take/return the drive. We request that it be returned within 3 days.
Researchers desiring help with data analysis on a fee for services basis can obtain support for analysis of their Agilent data through the BIOGEM Core (biogem@ucsd.edu).
Please note the following BIOGEM Policy for Illumina 1G Analyzer Sequencing:

The Investigator agrees that they solely are responsible for the quality of the sequencing library submitted. They are required to provide BIOGEM with the concentration of the sample and the OD260/280 ratio as outlined exactly in the online form. All samples and sequencing reagents will be delivered to the facility on dry ice only after coordinating a suitable drop off time with James Sprague . Please note BIOGEM is not responsible for replacing flow cells when the PhiX Quality Control for the sequencing run is valid. If a PhiX sequencing control is not run (at the option of the investigator), BIOGEM is not responsible for replacing flow cells.

Last Updated March 2009
By Dr. Gary Hardiman