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 include Illumina RNA-sequencing and Fluidigm high throughput real-time PCR. RNA-seq is used for whole transcriptome profiling and can be performed from a variety of sample types, including purified total RNA, small populations of sorted cells, or single cells. The Fluidigm real-time PCR platform is used for focused profiling and can also be performed on a variety of input types.

The Core laboratory uses an Illumina HiSeq2500 platform for next generation sequencing. The HiSeq2500 is a high-output member of Illumina’s HiSeq family of instruments. It can accomodate either 1 or 2 flowcells simultaneously, in either a high data output mode that can generate up to 2 billion sequence reads per flowcell or in a rapid mode that can generate 300 million reads. It is used in conjunction with the cBot clonal amplification system that immobilizes DNA fragments on a flowcell and grows the DNA clusters. Both RNA-seq and DNA-seq pipelines are possible, including, whole exome, whole genome, ChIP-seq, ATAC-seq, etc.

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 are two Fluidigm C1 Single Cell Preparation Systems, an on-chip capture and processing instrument, capable of capturing single cells and processing their RNA for analysis either by single cell RNA-seq on the HiSeq2500 or for qPCR on the Biomark HD. A NanoEnTek JuLI Stage Imager, a fully-automated, digital fluorescence live cell imager, is used to document cell capture on the C1 chips. The JuLI Stage is also able to remotely monitor cell culture in a CO2 incubator for a variety of applications.

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 and a Qubit fluorometer. An Illumina HiScan Reader, a high performance microarray scanner with sub-micron resolution, is available by special request.