Affymetrix GeneTitan system. The Affymetrix GeneTitan Multi-Channel (MC) Instrument is a fully-integrated microarray system ideal for expression and genotyping based applications. The GeneTitan system automates array processing from target hybridization to data generation by combining a hybridization oven, fluidics processing, and state-of-the art imaging device into a single bench-top instrument. The system is scalable and meets both medium- and high-throughput needs. The GeneTitan in GSL is compatible with the customizable Axiom Plate SNP genotyping arrays (96- and 384- array layouts), and also supports gene expression applications on 16-, 24-, 96-array layouts.
Illumina MiSeq system. The Illumina MiSeq Desktop Sequencer is a compact, all-in-one next-generation sequencing platform incorporating cluster generation, paired-end fluidics, sequencing by synthesis chemistry, and data analysis. The MiSeq system enables a broad range of applications and is ideal for focused applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression analysis, and more. The system in GSL is compatible with Illumina’s sample preparation methods which prepare input DNA or RNA for applications such as whole-genome sequencing, targeted region resequencing, transcriptome analysis, and expression profiling. The sequencing process takes place on a single flow cell and multiple samples can be run on the flow cell in parallel by using unique indices for each sample. The system in GSL can run both MiSeq V2- (up to 15 million reads) and V3-sequencing reagent kits (up to 25 million reads). Data management is streamlined with a connection to Illumina’s genomic computing environment, BaseSpace.
Illumina NextSeq 500 system. The Illumina NextSeq 500 system is a desktop next-generation sequencing (NGS) system that uses Illumina’s reversible-terminator sequencing by synthesis chemistry. The NextSeq 500 integrates cluster generation, sequencing by synthesis, and base calling into a single NGS system. The NextSeq 500 is a high output next-generation sequencing system which is scalable (up to 800 million reads) and can be adapted to perform applications ranging from mid-throughput to high-throughput sequencing applications such as exome, whole genome and transcriptome sequencing runs. Data management is streamlined with a connection to Illumina’s genomic computing environment, BaseSpace.
Biomek FX liquid handling system. The Biomek robotic workstation is outfitted with two independently programmable arms and has space on the work deck to accommodate 16 microtiter plates at a time. One arm is outfitted with a 96 tip head allowing pipetting in 96 well and 384 well formats. The second arm is outfitted with a Span-8 head that allows 8 channel pipetting with variable spacing for transfer of samples from tubes to plate configuration. A bar code reader allows the robot to identify plates on the deck and organize pipetting. This workstation, which is housed in a dedicated room, is used for pre-PCR sample manipulations including organizing working stocks in plate formats, normalizing concentrations of DNA samples and setup of reactions.
Tecan Freedom Evo robotic workstations. There are two of these 8 channel liquid sample handling workstations in the GSL. The workstations are specifically customized for use with the Illumina genotyping system and are fully outfitted with all necessary accessories for processing genotyping, expression, or methylation arrays.
Illumina BeadXpress system. The BeadXpress is a dual laser fluorescent scanner that is designed to be used with custom low to mid-plex Illumina arrays. These can include both genotyping and methylation arrays. The BeadXpress is most efficient for assays in the range of 48 to 384 SNPs or methylation sites.
Illumina BeadStation and iScan system. Illumina’s BeadStation system is a complete, bench-top solution for genetic analysis that enables a wide range of sample throughput and multiple applications. Both RNA and DNA-based applications are easily accessible on the system. The accompanying iScan is a dual laser fluorescent scanner dedicated for reading Illumina arrays. The model in the GSL is outfitted with a robotic autoloader that allows for unattended loading and scanning of arrays. The iScan reader is essential for reading high volume genotyping projects, i.e., those typically requiring more than 384 SNPs, as well as Illumina whole genome expression or methylation arrays. The iScan is typically used with standard arrays for whole genome analysis, custom arrays for mid to higher plex genotyping or methylation (i.e., greater than 384 sites) can also be designed and run on the iScan.
Ion Torrent Personal Genome Machine. The Ion Torrent is a new platform for focused next-generation sequencing. The instrument uses disposable semiconductor sequencing chips containing micro-machined wells that measure the pH change that occurs when a nucleotide is incorporated into a DNA strand. Chips with different numbers of features determine the sequencing capacity that can range from 10Mb to 1Gb depending on the model of chip selected. Applications include targeted resequencing of chromosomal regions or panels of genes, RNAseq for transcript quantitation, or ChIPseq for genome-wide profiling of protein-DNA interactions. Individual sequencing runs take 2 hours.
ABI7900HT Real-Time PCR system. The ABI7900 is used for both gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5′ nuclease (Taqman) assay. The instrument in the GSL has interchangeable 96 and 384 well blocks and an autoloader for large volume applications. This instrument is primarily used for low volume projects in which a small number of genes need to be assayed for expression or a limited number of SNPs (<48) genotyped.
Other ancillary equipment. The GSL has 4 BioRad Tetrad PCR machines each containing 4 independently programmable blocks with 18 alpha units in either 96 or 384 well format providing the equivalent of 16 PCR machines. For quantitation of DNA or RNA, a Nanodrop ND-8000 spectrophotometer is available. Quantitation can also be performed using Pico-Green or Ribo-Green on a Beckman DTX880 fluorescent plate reader.