Genomics Core Laboratory
The Genomics Core provides resources to BRI and external investigators for analysis, from sample processing through data generation, as well as basic bioinformatics analysis, provided by our Bioinformatics Group.
Currently available technologies focus on Illumina sequencing. RNA-seq is used primarily for whole transcriptome profiling and can be performed from a variety of sample types, including purified total RNA, cell populations (including low input samples), or single cells. DNA-seq pipelines can also be performed, including bulk and single cell ATAC-seq, ChIP-seq, whole exome, whole genome, etc.
The Core laboratory uses an Illumina HiSeq2500 platform for next generation sequencing. The HiSeq2500 is a 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.
Ancillary equipment for sample processing includes a 10x Genomics Chromium Controller, a Formulatrix Mantis Liquid Handler, a Qiagen QIAgility (also a liquid handling robot), an Agilent TapeStation 4200 and a Bioanalyzer 2100 (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.
Services are available to BRI and Virginia Mason investigators as well as outside investigators.