Technology

Roche GS-FLX (454) Next Generation Sequencing

The Roche Genome Sequencer FLX System (GS-FLX or “454”) moves DNA sequencing to a chip based platform dramatically reducing the work and price required for genome level sequencing projects. This is performed by simplifying the up front work required to generate and amplify a genomic library and by massive parallel sequencing on a fiber optic chip.  The 454 sequencer currently generates 1,000,000 reads per run at a current mean read length of 400-500 bp (~400 Mbp output per instrument run).  454 applications include: de novo sequencing; re-sequencing; discovery of small RNAs and detection of their relative abundances; detection of low-frequency (<5%) somatic mutations; uncovering the diversity in metagenomic samples; amplicon sequencing; and transcriptome sequencing.

• Amplicon Library Preparation Method Manual [PDF]
• Amplicon Fusion Primer Design Guidelines for GS FLX Titanium Series Lib-A Chemistry [PDF]

Solexa Next Generation Sequencing

Like the Roche GS-FLX sequencer the Solexa Genome Analyzer (GA) moves DNA sequencing to a chip based platform dramatically reducing the work and price required for genome level sequencing projects. An entire genomic library is amplified for sequencing simultaneously on a chip via bridge-PCR and then each clonally amplified product (cluster on the chip) is sequenced by synthesis on the Solexa GA by massive parallel sequencing across the entire chip (Solexa ‘flow cell’). During sequencing each terminating base is labeled with one of four fluorophores allowing for the reading of one base per sequencing cycle per cluster. Each Solexa GAII instrument generates 10-25 million reads at 18-100 bp per lane with eight lanes available per run.  Up to 40 billion bp of usable data can be generated on each Solexa GAIIx instrument per run when run with the Illumina Genome Analyzer Paired-End Module.  Applications on the Solexa platform include: genome sequencing and resequencing; transcriptome sequencing; amplicon sequencing; and ChIP-seq.

High-throughput Microarray Processing

The IGSB HGAC performs tiling and expression microarray hybridizations using the Tecan HS 4800 PRO Hybridization Station and the Agilent manual SureHyb protocol. Our facility has the current capacity to process 12 slides simultaneously on Tecan and 48 slides simultaneously following Agilent’s SureHyb protocol. To date we have processed Agilent arrays in a high-throughput format following Agilent’s Gene Expression or ChIP-seq protocols. We have two scanners, a single slide Axon 4000B 5um scanner and a C-version Agilent Autoloader scanner capable of scanning up to 48-slides at a maximum resolution of 2um.