Genotyping Services

For array based genotyping customers can select from the Illumina Infinium array portfolio including the MethylationEPIC array for epigenetic analyses and the HumanCytoSNP-12 array for detecting structural genomic variants. A complete list of arrays can be found here. 
Arrays are available in various formats, most commonly used are chips for 8, 12 and 24 samples. Customers need to provide an appropriate sample number to fill all places on the array. Please contact us for assistance with ordering Illumina genotyping array kits.
Bisulfite conversion required for the MethylationEPIC array is also available as a service. We use the Zymo EZ-96 DNA Methylation Kit.

DNA requirements 

The Illumina Infinium assay is very robust provided high-molecular-weight DNA is used. As heavily degraded DNA may lead to high failure rates, we recommend spot-checking samples on a 0.8% agarose gel to assess for degradation.
Acceptable sample concentration must be in the range of 50-100 ng/µl. We recommend measuring the concentration with a fluorescent dye (Picogreen, Qubit) and not with UV (Nanodrop) as this may lead to an overestimation of the DNA amount due to RNA or other contaminants.
The sample volume required depends on the array type but must be at least 10 µl. DNA can be suspended in water, Tris-HCl buffer or TE.
Samples must be delivered in standard skirted 96-well microtiter plates with no empty wells.

Data output and delivery

For all procesed samples basic quality checks will be performed using Illumina’s GenomeStudio software. Afterwards, customers will receive a link to download the raw data from the iScan scanner (.idat files) together with a sample sheet to re-analyze data on their own.

The core also offer full-service data analysis service using Illumina’s GenomeStudio software to export genotypes. The genotype data set is available for download in several formats depending on the customer’s request, which can be discussed during the initial project meeting.

Our Thermo Fisher SeqStudio Genetic Analyzer is a 4-capillary Sanger sequencer with a throughput of 48-192 samples per day depending on the selected run module. It is calibrated for the BigDye Terminator v3.1 Sanger sequencing kits and Dye Set G5 for fragment analysis applications. A calibration with other dyes is possible, please contact us if you need help with different dyes.

The SeqStudio analyzer can be used for diverse Sanger sequencing and fragment analysis applications for small to medium-sized projects. The instrument can be booked as full service (Sanger sequencing reactions including the PCR and all cleaning steps) or Run only with users submitting already prepared samples to the core. Please contact us these services for the first time. More details on the SeqSudio instrument can be found here.

Samples must be in 96-well microtiter plates and should be placed in a freezer. Any 96-well microtiter plate is acceptable as long as it is labeled with the user’s name, institute and date.
Sample volume must be > 30 µl if suspended in water or > 20 µl if suspended in at least 50% Hi-Di Formamide.

SeqStudio run only: Users will provide ready-to-run sequencing or fragment analysis reactions. The Core Facility team will load the sequencer and deliver data via a download link.

SeqStudio full service:  User must provide the DNA sample and appropriate primers. The core will perform the PCR and sequencing reactions with the customers primers using the BigDye Terminator v3.1 Sanger sequencing kit. All cleaning steps are included.

Our Thermo Fisher QuantStudio 7 Flex Real-Time PCR System is accessible to trained users for self service. Three different blocks are available: 96-well (0.2 ml), 384-well and TaqManArray card block. All blocks can easily be changed without any tools. A short introduction from the core team is mandatory for self service customers, please schedule a training prior to first use.

The instrument is located in building 34/room 102.

More details on the Quantstudio instrument can be found here.