The SOLiD System: Next-Generation Sequencing

1. The SOLiD System: Next-Generation Sequencing Overview of the SOLiD System – Scalable AccurateUltra High Throughput Flexible Mate Pairs

2. APPLICATIONS PERFORMED ON THE SOLiD • Genome • Transcriptome • Epigenome

3. GENOME • De Novo Sequencing • Targeted Resequencing • Whole Genome Resequencing

4. TRANSCRIPTOME • Gene Expression Profiling • Small RNA Analysis • Whole Transcriptome Analysis

5. EPIGENOME • Chromatin Immunoprecipitation Sequencing (ChIP-Seq) • Methylation Analysis

6. Log In - Sample Submission & Tracking Description Services Instruments Submitting Samples Pricing Software Frequently Asked Questions Next-Gen Sequencing Facility

7. Advantage over old technique : • Next-Gen sequencing platforms are so named because they are capable of generating billions of bases of sequence per run – magnitudes above the amount generated per the Sanger sequencing reaction method that has been widely used for over a decade. The ability to generate such a vast amount of sequence data in a short amount of time is quickly expanding the way that genomic research is performed and helping investigators discover biological information that was previously unattainable.

8. Description: • The SOLiD instrument utilizes a series of ligation and detection rounds to sequence millions of fragments simultaneously. There are five primer cycles performed on the instrument with each cycle staggered by a single base and including a series of seven or ten ligations for either a 35 or 50 base pair sequencing run. Each ligation decodes two bases and is recorded through fluorescent imaging. By compiling the fluorescent reads in color space for each fragment, an accurate sequence can be generated. A much more detailed description of the technology including videos, literature, and publications is available at the Applied Biosystems SOLiD System Sequencing page.

9. Services: • Two types of libraries are available for sequencing Fragment and Mate Pairs. • Fragment libraries include whole genome resequencing, targeted resequencing, RNA-seq, ChIP-seq, and small RNA libraries. • The Core performs a quantitative PCR (qPCR) assay on every library to determine its concentration. Using the information from the qPCR, the Core performs a series of emulsion PCRs (ePCR) to amplify template onto beads with individual fragments from the library (or pool of bar-coded libraries). • The completed ePCR then undergoes a breaking and enrichment procedure to release the templated beads from the oil mixture and to enrich for the templated beads that will be deposited onto slides to run in the SOLiD instrument. Before a full run is conducted in the SOLiD, a quality control run is performed to ensure that the ePCR and breaking worked properly. Once the beads pass the QC run, a full slide run is performed on the instrument. Upon completion, each customer is provided with the color space sequence data and run quality data.

10. Instruments: • Applied Biosystems SOLiD System Sequencer • Covaris S2 Sonicator • Applied Biosystems 9700 Thermal Cycler • Hydroshear

11. Submitting Samples: • To begin a Next-Gen sequencing project with the core, please contact mrfadm@umdnj.edu to arrange a consultation. Once project details have been coordinated, an account is created on our on-line Next-Gen Sequencing tracking system and samples can be submitted to the Core.

12. Template Requirements for Library Preparation: • Fragment Genomic DNA Library - • Small RNA Library – • Whole-Transcriptome Library – • Chromatin Immunoprecipitated DNA -

13. Pricing:

14. Software:

15. Frequently asked questions: