Genomics Platform

The Genomics Core provides resources to BRI and external investigators for gene expression analysis, from sample processing through data generation, as well as basic bioinformatics analysis, provided by our Bioinformatics Core Team. Currently available technologies for whole transcriptome profiling include Illumina microarray and RNA-sequencing.  Additionally, focused profiling is available using a Fluidigm high-throughput real-time PCR platform.

The Core laboratory uses an Illumina HiScanSQ platform for gene expression profiling. The HiScanSQ is a dual function instrument, combining a microarray scanner with a sequencing module. The HiScan Reader, a high performance array scanner with sub-micron resolution, can image bead arrays, as well as sequencing flow cells. The platform also includes the SQ module, an add-on fluidics device that delivers Illumina’s sequencing-by-synthesis reagents, and the cBot clonal amplification system that grows the DNA clusters.

Focused profiling is performed using a Fluidigm BioMark HD.  The Fluidigm Biomark HD leverages micro-fluidic technology to miniaturize qPCR reaction volumes down to a few nanoliters and allows over 9200 reactions to be run simultaneously with high precision.  Additionally, there is a Fluidigm C1 Single Cell Preparation System, an on-chip capture and processing instrument, capable of capturing single cells and processing their RNA for analysis either by qPCR on the Biomark HD or for single cell RNA-seq on the HiScan SQ.

Ancillary equipment for sample processing includes a Qiagen QIAgility (a fluid handling robot), an Agilent Bioanalyzer (to measure RNA/DNA integrity and size) and a Tecan NanoQuant (for high throughput sample quantitation). Additionally, there is an Applied Biosystems StepOne Plus Real-Time qPCR instrument.

Availability: Services are available to BRI and VMMC investigators as well as outside investigators.

Manager: Vivian Gersuk, PhD

Contact: For more information, please contact VGersuk@benaroyaresearch.org