Services of the Genomics Facility
Microarrays are the perfect option to investigate and determine which known genes and pathways may be involved in a biological response (to a treatment, to a disease, to cell development, etc.).
The Genomics Facility processes RNA and DNA for hybridisation to Affymetrix microarrays to investigate the transcriptional profiling in a wide range of organisms, on gene level, for splicing variants, and for miRNA. SNP analyses for human are also possible.
Each nucleic acid sample is analysed for its quality and quantity, amplified, fragmented, and terminally Biotin-labelled following established standardised protocols before being hybridised to a microarray. Hybridised nucleic acids will be visualised by PE-Streptoavidin detection of biotinylated nucleic acid, using a powerful high-resolution scanner.
The end user can either be provided with the "Cel" files containing all the experimental data required for their own bioinformatics analysis, or the Genomics Facility can provide data analysis for microarrays.
NGS is a very efficient tool in molecular biology, and can be used to analyse a wide range of DNA and RNA samples. NGS-based approaches have several strengths:
- A priori knowledge of the genome or genomic features is not necessary
- Single nucleotide resolution for detection of related genes or features, alternatively spliced transcripts, noncoding RNA, allelic gene variants and single nucleotide polymorphisms
- Higher dynamic range of signal
- Requires little DNA/RNA as input
Numerous applications and domains are possible with our NGS platform:
- RNA Sequencing (RNA-Seq – total RNA or mRNA)
- MicroRNA Sequencing (miRNA-Seq)
- Long Non-Coding RNA Sequencing (lncRNA-Seq)
- Single Cell RNA Sequencing (scRNA-Seq)
- Whole Genome Sequencing (WGS),
- Whole Exome Sequencing (WES),
- ChIP Sequencing (ChIP-Seq – analysis of protein interactions with DNA)
- Ampli-Seq (targeted resequencing)
- Methylation Sequencing (Methyl-Seq)
- DNase-Seq (identification of regulatory regions)
- ATAC-Seq (chromatin accessibility)
The Genomics Facility provides a complete and reliable set of expertise, with experimental consulting, sample and library preparation, quality control and data analysis. The platform proposes primary bioinformatics analyses to users and more advanced analyses.
See Bioinformatics section.
The Genomics Facility implements “state of the art” bioinformatics solutions to settle the big data problem, reduce analyses time and speed up biological research. We offer up-to-date and standardised data analysis workflows embedded in a generic, extendable bioinformatics environment.
We can also provide advanced bioinformatics support and downstream analysis. By archiving sequenced data, storing analyses results and metadata in our databases, we ensure a high level of reproducibility and allow for fast and parameterised reanalysis.
We provide tailor-made solutions for your NGS project at different levels:
- Consulting in bioinformatics terms.
- Microarray data analysis.
- Basic data analysis workflows for various NGS applications.
- Advanced bioinformatics support tailored to project specific needs.
- Development of analysis pipelines of emerging applications on request.
- Easy access to analysis results or online services through our web interface and time limited storage of sequence data.
- Recording of NGS- and MA-experiments and submission of results to GEO (Gene Expression Omnibus).
Users can benefit from the Genomics Facility’s expertise to construct additional services.
We provide the following services:
- DNA & RNA isolation by Maxwell RSC
- Nanodrop quantification of DNA & RNA
- Quantus quantification of DNA & RNA
- Tape Station quality control of DNA & RNA
- Bioanalyser quality control of DNA & RNA
- Fragmentation of DNA & RNA by Covaris
- PCR & RT-qPCR
Please contact us if you wish to use one of these services.