University of Southern California Epigenome Center Data Production Core

The Data Production Facility of the Epigenome Center operates a Hi-Seq 2000. This sequencer operates in both single read (SR) and paired end (PE) modes. Choosing which mode and number of cycles of sequencing (length of read) is a key first step in experimental design and is covered more fully in "Getting Started with NGS." 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 and consultation services 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.

Returning Users Go here to download your sample submission form.

Getting Started with NGS New and potential users should begin here, with information on how the process works, what types of sequencing options are available, and how these options could be applied to your project’s needs. Sample submission forms are also available from this page.

Making NGS Libraries This page provides information about making and analyzing libraries suitable for NGS, whether constructed by you or by us. This includes information about RNA-seq, ChIP-seq, targeted capture libraries, whole genome bisulfite libraries, and more.

Prices Latest fees for sequencing services.

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

Data Recovery and Analysis The guts of the whole process! This is the most challenging aspect of NGS and needs to be considered carefully before undertaking any actual sequencing runs. We recommend that at the outset of any project a bioinformaticist is included in the initial strategic discussions. This can be 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. everyone meeting together 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.