Genomics-RNA | MedUni Vienna

Our units

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.

The Genomics Core Facility offers complete workflows for bulk, single-cell, and spatial transcriptomics experiments. In addition, project-specific sequencing services are also available. The range of services includes project planning, laboratory implementation, as well as data analysis and interpretation. In addition, the CF Genomics is committed to education and training by organizing workshops, training sessions, and seminars on topics such as single-cell and spatial transcriptomics technologies, sample preparation, and bioinformatics methods.

Our services are available via our iLab-booking tool:
https://meduniwien.ilabsolutions.com/service_center/show_external/3673?name=muw-core-facilities

Our instruments

Services

Transcriptome analysis:

•    Illumina short read bulkRNA sequencing: mRNA, total RNA, QuantSeq, standard as well as as low input protocols

•    Oxford Nanopore Technologies long read sequencing: direct RNA, cDNA protocols

•    10x Genomics Visium Spatial Transcriptomics

•    10x Genomics single-cell gene expression protocols

•    10x Genomics Xenium in situ Spatial Transcriptomics

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

For Xenium in-situ experiments cell-feature matrices, transcripts and segmentation boundaries as well as tissue images will be delivered.

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.