Core Facility – nCCF nCounter Core Facility
The nCounter Core Facility offers state-of-the-art methods for mRNA and miRNA expression profiling (nCounter SPRINT Profiler), as well as Digital Spatial Profiling at the transcript level (GeoMx Digital Spatial Profiler) and protein level (GeoMx Digital Spatial Profiler, Lunaphore COMET). In addition, the facility provides various analytical methods for quality control of RNA and DNA samples.
The nCounter Core Facility was established in 2011 and is part of the CellNetworks Core Technology Platform at Heidelberg University and the MULTI-SPACE platform of the Health & Life Science Alliance. In the DFG’s research infrastructure portal RIsources, the nCounter Core Facility is listed under RI_00563 (nCounter SPRINT Profiler, GeoMX Digital Spatial Profiler) and RI_00613 (Lunaphore COMET).
For more information on our services, protocols, and latest updates, please visit our internal website.
Project Request
Our Services are available to:
- Heidelberg University, including the Medical Faculties of Heidelberg and Mannheim
- Heidelberg University Hospital
- Members of the Health & Life Science Alliance
- The HBIGS Graduate School (Hartmut Hoffmann Berling International Graduate School of Molecular and Cellular Biology)
- HMLS (Heidelberg Molecular Life Sciences)
- External academic institutions
- External commercial organizations
Initiating a Project Request
To initiate a project at the nCounter Core Facility, you must first register and submit a request via the inquiry and booking system iLab. Following this, a meeting with staff from the nCounter Core Facility (and NanoString) will be arranged to assess the project's feasibility and discuss the next steps.
Before a project can begin for institutions outside the Medical Faculty of Heidelberg, a contract must typically be established and processed by the Legal Department of Heidelberg University Hospital. All further steps are managed through the iLabs platform.
What Criteria must my Samples meet?
Please read our Terms of Use (nCounter SPRINT PROFILER/GeoMx Digital Spatial Profiler, Lunaphore COMET System).
If you have any further questions, please take a look at our General Guidelines.
Please direct any questions regarding analyses with the nCounter SPRINT Profiler and the GeoMx Digital Spatial Profiler to: Dipl. Ing. Ralph Röth at ralph.roeth@med.uni-heidelberg.de or n.counter@med.uni-heidelberg.de
Please direct any questions regarding analyses with the Lunaphore COMET System to: Dr. Esther Kimmle at Esther.Kimmle@med.uni-heidelberg.de
Fees
nCounter SPRINT Profiler / GeoMX Digital Spatial Profiler Analyses:
Please order the necessary analysis materials in advance from your designated contact person at nanoString Technologies / Bruker, in accordance with our single-use agreement. A service fee will be charged by the facility for all consumables, sample handling, quality control, as well as for data generation and processing. Please refer to the single-use agreement for a price overview.
Lunaphore COMET System Analyses:
A price overview can be found in the single-use agreement, and a detailed price quote will be provided after discussing your project. A service fee will be charged for all consumables, infrastructure, sample handling, and data processing.
Services & Equipment
The nCounter Sprint Profiler
The nCounter SPRINT Profiler from NanoString Technologies is suitable for digital expression analysis of up to 800 mRNAs or miRNAs as well as CNV analysis at DNA level.
For multiplex analysis, the device uses fluorescently labelled reporter probes, which are highly resistant to poor RNA quality due to their length of approx. 100 bases and are therefore ideal for samples that are difficult to analyse, such as FFPE (formalin-fixed, paraffin-embedded) samples.
The application of a unique coding technology enables the direct counting of single RNA molecules at all levels of biological expression, with a sensitivity and specificity comparable to Real Time PCR (RT PCR). In addition, only very small amounts of RNA (25-150ng) or DNA (150ng) are required for the analysis. Reverse transcription of the RNA is not required.
The SPRINT Profiler is a perfect system for the validation of microarrays, the analysis of signalling pathways, the expression analysis of defined gene lists (individual or predefined) as well as for the validation of biomarkers.
THE GEOMX DIGITAL SPATIAL PROFILER
For the creation of multicellular expression profiles at the transcript and protein level, the nCounter Core Facility offers the GeoMx Digital Spatial Profiler from NanoString Technologies. This system utilizes photocleavable oligonucleotide barcodes bound to antibodies or RNA probes, enabling nearly unlimited multiplexing (~20,000 RNAs, ≥100 proteins).
Additionally, the device allows for highly complex spatial resolution and quantification of proteins and RNA (Whole Transcriptome Readout).
QUALITY CONTROL
For dedicated quality control analyses, we use the Agilent TapeStation and the Qubit system from Thermo Fisher Scientific.
LUNAPHORE COMET PLATFORM
The Lunaphore COMET platform enables the simultaneous visualisation of up to 40 antibodies on one to four tissue samples. The automated workflow and a precise microfluidics system ensure high reproducibility. In addition to proteins, specific RNA samples can also be stained.
The tissue samples (FFPE or Fresh Frozen) are directly or indirectly stained and imaged. The background is automatically subtracted. The generated images are saved in tiff format and can therefore be analysed with common programs.
Workflow Lunaphore COMET platform:
After registering with and requesting a "Lunaphore COMET Consultation request" in iLabs, the project and the experiments are discussed. After completing the "Lunaphore COMET sample run" request in iLabs and sending all required materials and samples, test runs are carried out first and then the experiments themselves after further discussion. The data can then be collected or downloaded as agreed.
Team
Table
| Dr. rer. nat. Stefanie Mellein
stefanie.mellein@med.uni-heidelberg.de |
| Dipl. Ing. Ralph Röth Administrative contact, nCounter SPRINT Profiler/GeoMX Digital Spatial Profiler, Sample QC
ralph.roeth@med.uni-heidelberg.de |
| Heike Kuzan nCounter SPRINT Profiler/GeoMX Digital Spatial Profiler, Sample QC
heike.kuzan@med.uni-heidelberg.de |
Dr. sc. nat. Denis Schapiro Project Manager Lunaphore COMET (scientific contact person) Institute for Computational Biomedicine | |
Dr. rer. nat. Esther Kimmle Administrative contact Lunaphore COMET Institute for Computational Biomedicine esther.kimmle@uni-heidelberg.de +49 6221 56-311563 |
Selected publications
Table
An extensive list of our publications can be found here:
Funding Resources
