Please contact Charles Nicolet, Ph.D. for further information on Next Generation Sequencing services.

We specialize in whole genome bisulfite sequencing!

Returning Users: Sample Submission Form [pdf | doc]

Using a massively parallel sequencing approach, the Illumina sequencing instruments in the Data Production Core generate gigabases of high quality sequence data for each sample. The system uses Solexa sequencing technology and novel reversible terminator chemistry, optimized to achieve unprecedented levels of cost effectiveness and throughput. A good place to start is the IIllumina website where you can find more information describing this instrument and its application, and the sample preparation kits.

The Data Production Facility of the Epigenome Center operates three sequencing instruments: two GAIIX and one Hi-Seq. Both platform types produce data of comparable quality, the main difference is the Hi-Seq has a greater capacity and provides more sequence for comparable cost. All our sequencers have the ability to perform paired end reads. Data produced from such paired end reads greatly facilitates assemblies and investigation of genomic structure and this capability, coupled with chemistry improvements allowing longer accurate reads, has expanded the utility of these “short-read” platforms for de novo assemblies. Illumina maintains a publication site with the most up-to-date citations about the experiments being done with these instruments. In addition, we’re always available to discuss what we can do to facilitate your research which includes potential R & D opportunities. Our sequencing capabilities are available to members of the Cancer Center at reduced cost, but are also available to all USC researchers, as well as off-campus users at both academic centers and businesses.

Steps involved in a sequencing experiment can be broken down into a series of experimental manipulations, instrument runs, and data analyses. These steps include creation of a sequencing library, seeding and preparation of the flow cell, sequencing by synthesis, and bioinformatics. Follow the links below to find out more about the technology, about making libraries, bioinformatics, and getting started.

Returning Users Go here to download your sample submission form if you already have an account at the Cancer Center and have sequenced with us before.

Getting Started New users should begin here, with instructions about setting up a Cancer Center account (required for all users), and acquiring a sample drop off form. There is also information about how the process works, what types of sequencing options are available, and how the different options could be applied to your project’s needs.

Making Libraries This link provides access to information about making libraries suitable for sequencing, whether you wish to do it yourselves or whether you wish to do it with us. Links and information are provided about various kinds of libraries including mRNA-seq, ChIP-seq, regionally enriched libraries, smRNA, etc.

Prices Latest fees for sequencing services.

Sample Submission Guidelines A summary of the procedures for dropping off both ready to sequence libraries and raw materials for us to construct your libraries.

Data Recovery and Analysis The guts of the whole process! This is the part of sequencing to really think hard about. We recommend at the outset of any project that a bioinformaticist is included in the strategic discussions, either the people here in the Epigenome Center who can be hired for projects, or by the people in your lab or collaborative group who will be doing the analyses. This will help ensure that the sequencing runs carried out are the most relevant for the desired project goals. It will also help determine the project timeline, as the sequencing part is in many ways is the fastest and easiest part of the study.