Illumina Software to support the GAII-X system

Brown University
Illumina Software to support the GAII-X system


Thank you for your interest in Next Generation Sequencing at Brown University. The following information is intended to provide users with an introduction on how to get started with plans for a sequencing project.

The Genomics Core Facility, located at 70 Ship Street in the Laboratories for Molecular Medicine, is performing high throughput sequencing using Illumina instruments.

The Genomics Core Facility introduced Next Generation Sequencing Service (NGS) in June 2010 with a GAIIx sequencer. In April 2011, we expanded our successful service and we now exclusively operate the HiSeq2000. For more information on our instruments go to the link "HiSeq2000". In Spring 2013, we will upgrade the HiSeq2000 to the HiSeq2500.

The "Overview of Illumina Sequencing" link contains a helpful summary of the sequencing work flow and applications. (Thanks to Adrian Reich of the Wessel lab for providing this resource.) A lot of useful information can also be found under the "NGS FAQ" link.

For an introduction to the Illumina technology, please view the seminar content presented by Mike Smith of Illumina in May 2010 (under "Seminars" link, Brown log in required).

Browse the protocols under "Illumina Software" link for information on library preparation. The Core Facility accepts user prepared libraries for sequencing. We do not yet offer library preparation as part of our service. HiSeq compatible library preparation can be provided as a fee for service at URI. However, we can direct you to several users at Brown with extensive experience in library preparation using different methods.

Read the "Sample Submission Guideleines" link which describes how to submit your library samples to us for sequencing. If you are sending samples from off campus, please contact the Core Facility (401-863-2875) for shipment instructions.

Sign up for the Listserv/Discussion group by following instructions on this link. This is a forum to communicate run status and plan future runs.

Please note our policy for run order. Sequencing runs are executed in the order in which:

  1. samples are received by the Core facility (with sample submission form please),
  2. these samples pass QC (bioanalyzer and qPCR), and
  3. the flow cells are filled for a particular run.
  • For example, you have submitted 3 samples for a 35 base pair single read run. When we receive another 4 samples for 35 base pair single read run, and all 7 pass QC, the run begins as soon as the machine is free. The Listserv announcements will provide you with up to date information on when runs are completed and when the next run is expected to start.
  • Please contact us with your plans to do sequencing, as this helps us stock inventory of reagents accordingly. See the "Contact" tab under Genomics Core website for our information.