Applications

The GDC is a shared facility to provide its users a managed laboratory for DNA/RNA/protein extraction and quantification, DNA amplification, sequencing, and genotyping as well as data analysis mostly for non-model organism. A special focus is on high throughput technologies to cope with the increasing number of individuals and markers needed. Since 2012 we also offer library preparation for different Next Generation Sequencing platforms. Below a list of the main instruments available at the GDC.

List of Applications

Library preparation for Next (New) Generation Sequencing

We provide library preparation support for Illumina and PacBio sequencing platforms. If you want to prepare libraries for other NGS platforms (e.g. 454 or Iontorrent), please contact us.
For RADtaq sequencing we have primers and adapters in stock. We have 24 different barcoded P1 Adapter and several barcoded P2 Adapter available which we offer in small aliquots.

The following sizing and size selection tools are available:

• Covaris S220 AFA System
• Caliper size selections tool
• 2100 Bioanalyzer (Agilent)

DNA / RNA / protein extraction

• BeadRuptor (Omni)
• Retsch Mill (96-well plate and Eppendorf tubes)
• Tecan Genesis pro
• Bead dispenser: a simple and easily way to distribute beads into 96-well plates
• Thermo shaker: for 96-well plates and individual Eppendorf tubes
• We offer various extractions kits from different vendors (Machery Nagel, Zymo, Qiagen, LC Genomics) and different protocols are available to help you find the best extraction method for your study organism.

DNA/RNA quantification

• UV-Vis Spectrometer: 8-capillary NanoDrop 8000 (Thermo Scientific)
• Electrophoresis applications: 2100 Bioanalyzer (Agilent Technologies)
• Fluorometer: Qubit (Invitrogen)
• SlingShot kit: BioMark (Fluidigm)

PCR amplification 

• In total 9 PCR thermocycler (Labcycler (Sensoquest) and GeneAmp PCR System 9700 (ABI)) are available including a gradient thermocycler

Fragment analysis (e.g. Microsatellites, AFLP)

• 3730xl DNA Analyzer (48-capillary)
• 3130xl DNA Analyzer (16-capillary)

Sequencing

• Illumina: MiSeq
• Sanger sequencing: 3730xl DNA Analyzer (48-capillary)
• Sanger sequencing: 3130xl DNA Analyzer (16-capillary)
• Pyrosequencing: PyroMark ID (Qiagen)
• Targeted Resequencing: BioMark (Fluidigm)

SNP Genotyping

• SNP analysis and allele quantification: PyroMark ID (Qiagen)
• High throughput SNP genotyping: BioMark (Fluidigm)
• SNP genotyping (TaqMan probe, high resolution melt curve analysis (HRM)): 7500 FAST Real Time PCR System (ABI)
• SNPlex: 3730xl DNA Analyzer (48-capillary)
  

Gene expression analysis

• High throughput gene expression analysis (TaqMan probe, Evagreen): BioMark (Fluidigm)
• Gene expression analysis (TaqMan probe, SYBR Green): 7500 FAST Real Time PCR System (ABI)
  

Copy number variation

• BioMark (Fluidigm)

CpG methylation analysis

• PyroMark ID (Qiagen)

Data analysis

Three data analysis computers with various applications are available for our users. The software packages include GeneMapper, Assay Design, Sequencher, CLC Genomics Workbench, Geneious, 454 Newbler, and SMRT portal.

We also maintain a Sequencher (DNA analysis and assembly software) and Geneious network license that is available for PC and Mac users.

Users are also able to access the GDC internal computing environment. Currently the GDC has the following two Linux computers for computational biology and data storage:

• 24-core, 160 GB RAM workstation
• 40-core, 380 GB RAM server
• 11.5 TB storage server
• 12 TB Backup server

Please contact Stefan Zoller or Jean-Claude Walser if you have questions about the GDC computing environment or if you have special software requests.