TUCF introduces High-Throughput DNA Sequencing, also known as Next Generation or Deep Sequencing, using an Illumina Genome Analyzer II. The Genome Analyzer system can generate highly accurate results in under a week for discoveries in genomics, epigenomics, gene expression analysis, and protein-nucleic acid interactions.

The Genome Analyzer system is powered by Illumina Sequencing Technology, which uses a massively parallel sequencing-by-synthesis approach to generate billions of bases of high-quality DNA sequence per run.

Applications include:

• Genome Sequencing: De Novo Sequencing, Resequencing
• Deep Sequencing of Microbiomes
• Chromatin IP analysis (ChIP-Seq)
• Transcriptome Analysis (RNA-Seq): Profiling and Discovery
• Digital Gene Expression
• Small RNA/miRNA Identification and Quantitation
• DNA Methylation analysis

Download the High-Throughput Sequencing Order Form

Service

Currently we offer 36 nucleotide single reads or 72 nucleotide (36x2) paired-end reads. All sequence data, including reads mapped to a reference genome, will be provided on a DVD. Sequence data is archived on our server for one year. Additional bioinformatics support is available free to all Tufts users. We also offer bioinformatics consultations and support to institutions at an hourly rate.

All samples will be entered into a queue on receipt, and then scheduled for the next available run. At current levels, your samples will be run within 1-2 weeks. Once your run has started, turnaround time will be about a week.

Please contact Kip Bodi or Michael Berne to initiate requests for sequencing, scheduling, or other information.

Charges

All charges are per lane. Prices are effective as of August 1st, 2009.

Tufts and Tufts Medical Center

All Other Institutions

Sample Preparation

We expect submitted samples to be prepared ro run on the GA_II system. DNA Libraries should be gel purified and OD'd by spec after purification. We also request a picture of an aliquot run on a 2% TAE agarose gel with 100bp ladder markers. Alternately, you may provide the results file from an Agilent Bioanalyzer, with your peaks and concentrations clearly marked. If your sample concentration is over 100nM, please dilute to 100nM prior to shipping.

We also offer Genomic DNA Sample preparation using the TUCF protocol below. If you are interested in this service, please contact us for more details.

TUCF Protocol
This protocol will work for both single and paired-end libraries. On request, we can provide the adapters needed for this protocol.

• Modified Protocol for Paired-End Library Construction
  

Illumina Protocols
These are the protocols included with Illumina's standard kits. Please contact Illumina for pricing.

• Sequencing Genomic DNA
• Paired-End Sequencing
• Multiplexed Paired-End Sequencing
• ChIP Sequencing of DNA
• Sequencing of mRNA
• Analysis of Small RNA
• Digital Gene Expression-Tag Profiling with DpnII
• Digital Gene Expression-Tag Profiling with NlaIII

Shipping

Please ship your samples on dry ice, overnight to:

Michael Berne
Tufts University School of Medicine
Dept. of Physiology / Stearns 808
136 Harrison Ave.
Boston, MA 02111
Phone: (617) 636-2422
Fax: (617) 636-6737

Additional Documentation

• Genome Analyzer_II System Specifications
• ChIP-Seq Data Analysis
• Genomic Sequencing Data Analysis
• mRNA Expression Analysis

For more information about the Genome Analyzer II, please go to
www.illumina.com

Contact

For all questions about the service, please contact:

Kip Lord Bodi Jr.
Computational Biologist
Tufts University School of Medicine
136 Harrison Avenue, South Cove 502
Boston, MA 02111
617-636-3763
kip.bodi@tufts.edu