The CGRB began offering the Illumina/Solexa high throughput DNA sequencing service in 2007 on the Genome Analyzer (GA). In mid 2011 the GAIIx was retired and replaced with the higher throughput HiSeq 2000 instrument. The increased output of the HiSeq 2000 is due to the larger flow cell, the ability of the instrument to read sequence off both surfaces of the flow cell, and the capability to run two flow cells at the same time (like having 2 instruments). The HiSeq 2000 can be used for a variety of applications. The sequencing process takes place on a flow cell with 8 channels (one channel must be used for a PhiX control DNA), each of which may contain a different sample (or many samples if multiplexing). In early 2011 Illumina released v.3 kits, in which the amount of data that can be produced increased 3x. With v.3 kits the HiSeq 2000 can produce > 187.5 million reads or 37.5 Gb per lane. Actual output can vary depending on cluster density, but a typical run should produce >150 million filtered reads.
Illumina sells the following sample prep kits depending on the application: TruSeq™ DNA, TruSeq™ RNA, TruSeq™ Stranded RNA, TruSeq™ Small RNA, Nextera™ Mate Pair, Nextera™ DNA, Nextera XT™(for small genomes), and TruSeq™ ChIP-Seq. The newer TruSeq™ and Nextera™ reagents contain indexes for multiplexing. Sample prep reagents can be purchased directly from Illumina or from the Core Lab if less than one kit (48 samples) is needed. As of March 2013, the Core Lab offers TruSeq DNA, RNA, stranded RNA, and ChIP-seq library preparation as an optional service (Nextera XT and mate pair will be offered soon). Other vendors of compatible sample prep kits include NuGen Encore™ & Ovation®, Bioo Scientific NEXTflex™, and New England BioLabs NEBNext®. Please contact Mark Dasenko for more information and assistance with getting started. Additionally, please be well aware of the quantity of sequence data that will be generated during a run. This will require significant computational power and expertise.
The CGRB will provide a number of service, software, and hardware tools to facilitate capture and analysis of data. However, each group should consider their long-term computational programming and utilization needs, and plan accordingly with personnel. To help the OSU Illumina and Roche 454 HTS user community, we have established an HTS mailing list where users can share information and announcements are posted by the Core Lab. To join the HTS mailing list please subscribe or contact Mark Dasenko.
An overview of the Illumina HTS workflow and approximate durations of steps for a typical run are provided below:
Please note that as of March 2011, Illumina only supports 100bp reads on the HiSeq 2000.