Skip to main content Deutsch


The Core Facility Genomics is a service facility for characterizing genetic causes of widespread diseases using state-of-the-art, genome-wide, high-throughput analyses, and is available to all clinical departments and institutes & centers of the Medical University of Vienna.

At the Core Facility Genomics, a wide variety of transcriptome analyses are performed, such as small RNA-Seq, bulk RNA-Seq, single-cell as well as spatial RNA-Seq in addition to sequencing of gene panels and amplicons.

For this purpose, Illumina and Oxford Nanopore sequencing technologies are frequently used, among others.

Our range of services includes project planning, laboratory implementation as well as data analysis and help with interpretation. Our employees are happy to answer any questions.


Our services are available via our iLab-booking tool:



Transcriptome analysis:

  • Illumina short read bulkRNA sequencing: mRNA, total RNA, QuantSeq, small RNA, low input protocols
  • Oxford Nanopore Technologies long read sequencing: direct RNA, cDNA protocols
  • 10x Genomics Visium Spatial Transcriptomics: Fresh Frozen & FFPE
  • 10x Genomics single-cell gene expression protocols

Genome Analysis:

  • Amplicon and gene panels

Data analysis:
For all experiments, the raw sequencing data can be made available on the Illumina platform immediately after completion of the sequencing:

  • Intensities in Illumina .bcl format
  • The files generated from the intensities with the sequences of each sequenced fragment (reads) in .fastq format

Depending on the requirements of the experiment and the wishes of the project management, we carry out an initial analysis based on the fastq files. This includes:

  • Alignment against a reference genome with STAR aligner
  • Determination of raw expression values (counts)
  • Differential expression analysis (comparison of 2 or more groups of samples) with DESeq2 or other suitable analysis programs

The results of this first analysis are made available, for example:

  • The alignment files in .bam format
  • The raw counts per gene or per isoform per sample as a table
  • The results of the differential expression analysis as a table, e.g. fold-change and p-values per gene

Further analyses based on these results can be discussed and processed. These analyses will then take place on a collaborative basis: We are happy to develop project-specific analysis protocols, carry out analyses of over-represented pathways, GO terms, etc. (enrichment analysis), create plots, heat maps, figures, etc. and expect the results we generate and Representations an integration into resulting publications as co-authors.

Assoc. Prof. Priv.-Doz. Mag. Dr. Martin Bilban

Head of CF Genomics-RNA

Catarina de Almeida Diogo de Bettencourt e Ávila, MSc


Markus Jeitler, BSc


Annika Veselinovic