Genomics Facility
Head of Genomics Facility & Lab Manager
Andrea Rinaldi, PhD
andrea.rinaldi@ior.usi.ch, +41 58 666 7041
Members
Andrea Rinaldi, PhD
Lorenzo Scalise, Lab Technician
Overview
The IOR Genomics Facility is fully equipped to perform genomic studies, including next-generation sequencing (NGS) for DNA and RNA analyses. State of the art equipment include Illumina NextSeq, Illumina MiSeq, HTG EdgeSeq System, Bio-Rad QX200, Covaris M220 and 2100 Bioanalyzer. The Facility personnel provides support for experimental planning and performs quality control procedures required for NGS on Illumina’s platforms.
The services include sample preparation, data generation and, on request, delivery of partially preprocessed or analyzed sequencing data. Currently, we support the library construction for RNA-Sequencing (polyA and Ribozero), Whole Exon Sequencing (WES), Whole Genome Sequencing (WGS), small RNA-Sequencing, ChIP-Sequencing, Methyl-Sequencing, and amplicon sequencing.
The Facility provides support for genomic studies primarily to the researchers at the IOR, IRB and other Institutes in Ticino. The facility can also support a limited number of external collaborations. Our goal is to make next-generation sequencing and high-throughput screening accessible to as many researchers as possible. By doing so, we not only advance the use of these experimental techniques but also facilitate discoveries that are only possible using high-throughput technologies.
Key Equipment
- The illumina NextSeq 500 benchtop sequencing system provides the flexible power and simplicity you need to analyze whole genomes, exomes, and transcriptomes. The NextSeq generates up to 400 million reads, 2×150 bp paired-end reads, or 120 Gb of sequence data.
- The illumina MiSeq sequencing by synthesis chemistry is the most widely adopted next-generation sequencing technology. Data quality is achieved by a proprietary, reversible terminator-based method that detects single bases as they are incorporated into massively parallel DNA strands. The MiSeq generates up to 25 million, 2 x 300 bp paired-end reads, or 10 Gb of sequence data.
- The illumina MiniSeq System offers a simple, affordable solution. Advance your research with proven Illumina NGS technology. Perform a broad range of targeted DNA and RNA applications in your own lab on your own schedule.
- HTG EdgeSeq System LINK TO www.htgmolecular.com
- Bio-Rad QX200 LINK TO http://www.bio-rad.com/en-ch/product/qx200-droplet-digital-pcr-system?ID=MPOQQE4VY
- Covaris M220 – The Covaris is a DNA/RNA shearing method that uses Adaptive Focused Acoustics (AFA) technology under isothermal conditions to maintain the integrity of the nucleic acid sample. Mechanical shearing with AFA technology is the gold standard for nucleic acid fragmentation during DNA library preparation
- The 2100 Bioanalyzer from Agilent is essentially a capillary electrophoresis machine that utilizes lab-on-a-chip technology to perform many different separation assays. The assays are very quick and easy to set-up, compared to the large-scale gels normally required or these procedures.
Applications include:
- RNA integrity analysis
- DNA separation and sizing (genotyping, PCR products, etc)
- Protein separation and sizing
Key to the technology is the Agilent LabChips, which allow analysis of up to 12 samples in a single batch. The LabChips themselves are precision glass chips with a network of fine micro-capillaries etched onto the surface. A gel consisting of linear polyacrylamide (LPA) is cast into the capillaries, then, after running buffer is added, the samples are loaded onto the chip ready for electrophoresis.
The facility is supported by the Foundation fot the Institute of Oncology Research.
