Omics Data Analysis

Genome annotation is the process of defining functional elements such as genes, promotors, enhancers etc. within the sequence of a genome. As the annotation of many genomes becomes outdated over time re-annotation is being performed.

The 3D structure of the genome is crucial for the regulation of genetic processes since it can provide a spatial proximity between linear separated genetic regions. HiC aims to isolate these interacting gene loci for gaining knowledge about regulatory processes.

With the assay of transposase accessible chromatin sequencing (ATAC) accessible regions can be identified which gives information about active gene loci in different cell stages of both diseased and healthy cells.

DNA–protein interactions are essential for several molecular and cellular mechanisms, such as transcription, transcriptional regulation, DNA modifications etc.. Chromatin immunoprecipitation (ChIP) is a powerful method to investigate these interactions.

Methylation at the N6 position in adenosine (m6A) is the most common internal modification in eukaryotic RNAs. It has been shown to play a significant role in regulating processes connected to RNA and can be analysed through different methylation specific sequencing approaches, like m6A-seq or m6A-CLIP.

Histone modifications are key epigenetic regulators, controlling chromatin structure and thereby gene transcription. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the method of choice for identifying loci which are enriched for certain histone marks. We provide analysis of ChIP-seq data generated for most common histone marks.

DNA methylation plays a critical role in cellular differentiation, genomic imprinting, development and disease. The most widely used method for determining genome-wide DNA methylation patterns is bisulfite sequencing. We provide genome-wide analysis of DNA methylation from whole genome bisulfite-sequencing and reduced representation bisulfite sequencing data.

Quantifying RNA editing is crucial for gaining a better understanding of how these RNA modifications might impact and regulate downstream biological processes such as translation efficiency, RNA stability and alternative splicing. We offer analysis of RNA-Seq data for transcriptome-wide identification of both A-to-I and C-to-U RNA-editing events.

RNA-binding proteins (RBPs) play a critical role in the RNA maturation process. Analysis of RBP binding sites and modes therefore provides important information about the maturation or functional state of RNA as well as the cellular status. We routinely analyse CLIP-Seq data generated by the most common CLIP-Seq protocol variants.

Nascent RNA-sequencing techniques allow robust quantification of changes in RNA synthesis instead of monitoring steady state RNA levels. We offer detailed analysis of all common nascent RNA sequencing technologies, addressing nascent RNA expression.

Investigation of translation gives important insights in regulation of gene expression underlying diverse and complex biological processes. Ribosome profiling is the method of choice to globally analyse translation in vivo. We routinely provide analysis of data sets generated by ribosome profiling.

Alternative pre-mRNA splicing (AS) is a process resulting in the generation of multiple mRNA isoforms from one precursor, providing an additional layer of gene expression regulation. We offer comprehensive analysis of alternative splicing from bulk RNA-Seq data and long-read sequencing approaches.

Gene expression is the fundamental biological process by which genetic information is transmitted into a functional gene product. We routinely analyse differential gene expression from bulk or single cell RNA-Seq data.