Genomics Core Laboratory
The Genomics Core provides resources to BRI and external investigators for genomics analysis, from sample processing through data generation, as well as basic bioinformatics analysis, provided by our Bioinformatics Core Team.
Currently available technologies focus on Illumina RNA and DNA sequencing from purified nucleic acid, sorted cell populations, or single cells. 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 of 100-1000 cells), or single cells (both plate-sorted rare populations and high-throughput single-cell analyses). DNA-seq pipelines can also be performed, including bulk and single cell CUT&Tag/CUT&RUN, ATAC-seq, whole exome, and whole genome.
The Core laboratory houses three Illumina sequencers, a HiSeq2500, a NextSeq2000, and a Miseq. The HiSeq2500 can accommodate either 1 or 2 flowcells simultaneously, and can be run in a high data output mode that generates 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. The newly-released NextSeq2000 uses patterned flowcell technology and currently runs a 400M read flowcell. A 1000M read flowcell is expected to be released later this year. The MiSeq has a variety of flowcells sizes, from 1M to 25M reads and can perform long reads, up to 2 x 300bp.
Additionally, the Core offers single cell sequencing using a 10x Genomics Chromium Controller for high throughput single cell capture and processing. Other available equipment includes a ThermoFisher Kingfisher Flex, which extracts nucleic acid from a variety of samples, using magnetic bead technology, with a throughput of up to 96 samples. Two Qiagen QIAcube Connect instruments automate extraction of nucleic acid using spin column technology. A ThermoFisher QuantStudio 3D is available for digital PCR analysis for molecular quantitation. Ancillary equipment for sample processing includes a Formulatrix Mantis Liquid Handler, a Qiagen QIAgility (also a liquid handling robot), an Agilent TapeStation 4200, 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.