Research centers and equipment
Interdisciplinary research centers promote cooperation across disciplines and accelerate the translation of basic research results into new treatment methods.
The Translational Research Center (TRC), opened in 2014, features an examplary concept and infrastructure. This research building enables phyisicnas and basic scientists for collaborate closely and develop novel approaches for diagnosing and treating diseases. Currently, experts from the fields of inflammation, tumor, kidney and circulation research work in this building. While some labs are assigned permanently, others are others are made available to rotating clinical research groups.
Core units are centralized technological platforms available to all researchers at the Faculty. Qualified staff support the researchers.
This core unit offers operator-supported cell sorting via a MoFlo-(Beckman Coulter), Astrios (Beckman Coulter) and a FACS AriaII-(Beckton Dickinson) cell-sorter, access to two associated analytical devices (LSR Fortessa and CantoII, Beckton Dickinson) and immunomonitoring services at three locations in Erlangen. It is open to all employees at FAU and Universitätsklinikum Erlangen.
Head of laboratory: Dr. Arif B. Ekici
The Next Generation Sequencing Core Unit (NGS-CU) is run by the Faculty of Medicine and operated by the Institute of Human Genetics. The aim of the CU is to provide cost-effective and time-efficient use of state-of-the-art technology for genomic analyses in combination with guidance on experimental design and support in data analysis.
What we offer
We provide NGS-technology for researchers from Erlangen University Hospital, Institutes and Departments of Friedrich-Alexander University (FAU), but also for external research collaborators. The service spectrum also includes guidance on experimental design and the subsequent (primary) data analysis. We cover a wide range of different genomic analyses, e.g. whole transcriptome, whole methylome, ChIP and ATAC sequencing. Recently we added single-cell transcriptome analyses (single cell RNASeq) on our Chromium platform (10xGenomics).
What are we doing exactly?
After receipt of biological materials to be analyzed we perform quality control, different enrichment and depletion methods, preparation of sequencing libraries and sequencing of these libraries, depending of the specific questions. We perform data analysis in close collaboration with users. Our experiments are run on a HiSeq-2500 platform (Illumina). We have extensive experience such in bioinformatic analyses and have developed a robust and reliable pipeline followed by project-specific analyses depending on the experimental requirements.
Most RNA handed to us are from Qiagen- or phenol-based extraction protocols. Pooling of biological replicates does not affect the laboratory processing, but during data analysis, one can only make a summary statement. Accordingly, this is done only when there is insufficient material, e.g. sorted cells, too few cells in laser capture microdissection etc..
For the total RNA samples given to us, we perform quality control (Agilent BioAnalyzer) and will report QC results back to users. When the quality is sufficient, we will create the sequencing libraries and perform the sequencing. Data analysis is carried out in close consultation with users and we are ready to accommodate most specific requests on graphical presentation of results.
- The RNA samples should be total RNA samples to ensure reliable quality control. We need information on volume, quantity, concentration and other QC data, if available.
- All RNA should be DNAse digested, reliably and thoroughly. Please list the method.
- For all samples, you should give us further information such as species, tissue, for cell cultures also the cell type, in sorted cells, the approx. cell number.
- Are transcripts from an additional organism to be expected, e.g. as a result of transfection?
- All sample names should be as short as possible and identical in the supplied data forms and on the tube labels.
- Is there a preferred reference or a preferred gene model? We use by default: hg19/38, mm38, Rnor5/6 and the most recent Ensembl gene model.
- Which pair- or block-wise comparisons of samples make sense? Please define sample groups for data analysis!
- Are certain genes with differential expression known as positive controls (e.g., tested by qPCR)?
- Is a very high or very low number of expressed genes suspected?
- Are batch effects known? If yes, which samples belong to which batches?
- Sample-ID (as on the tubes)
- Extraction type (kit)
What do the analyses cost?
We charge costs for consumables and a contribution towards costs for project-related personnel. These prices only apply to projects from the University Hospital or FAU, as this is a service subsidized by the faculty. The cost varies depending on specific research questions. Frequently requested analyses and their costs are:
- 10xGenomics Single Cell-RNA-Seq (5.000 Cells, 20,000 reads/cell): 3,950 €
- RNA-Seq, bulk, 3‘-DGE, single end: 450 €
- RNA-Seq, bulk, single read: 600 €
- RNA-Seq, bulk, paired-end: 800 €
- ChIP-Seq/ATAC-Seq (after enrichment by users): 400 €
These costs include the preparation and provision of the data in a suitable form for the user’s own further analysis. This service requires no formal cooperation, an acknowledgment would be appropriate. Further detailed specific data analyses on a collaborative basis are of course possible and, in fact, frequently used.
Billing and settlement take place via internal cost allocation. We will send you an appropriate form with the number of samples noted. You then return this form to us, signed and with your cost account specified. For projects from the University, we issue an invoice instead.
For projects from outside Erlangen, other prices apply, which will then also include VAT. Please contact us for further information:
Apart from the core units, researchers can access cost-intensive methods and technologies via the following device platforms.
Genetic and genomic studies for complex traits and clinical studies require high quality DNA-samples of probands as well as a rigorous and reliable handling and tracking of large numbers of samples. Starting in 2009, the IZKF core facility Z4 “DNA-Extraktionsplattform (Biobank)” was established to offer quality controlled DNA-extraction from blood samples and other body fluids, their handling and aliquoting as well as their long-term archiving. The Core Unit has two large scale semi-automatic DNA-extraction platforms, a chemagic magnetic separation module I(Perkin Elmer) and an Autopure LS (Qiagen) and has a capacity of up to 10,000 samples/year. Both platforms yield high quality DNA samples suitable for all downstream applications such as PCR, SNP genotyping, microarray applications and next-generation sequencing. Part of the instrumentation was co-funded by FAU’s Comprehensive Cancer Center. After conclusion of the IZKF funding in 2013 the core facility continues to offer its services financed through user fees.