Introduction

The Bioinformatics Unit at IJC provides both internal and external researchers with high-quality computational analysis services covering all project aspects related to clinical and biological data. This includes experimental design and data analysis for microarray experiments and Next Generation Sequencing, statistical consulting, data integration, interpretation and reporting, and software development and data management. Our unit works closely with the Genomic Unit and the Single Cell Unit.

Services

• Bioinformatic data analysis (see below)

• Custom analyses and tailored software development

• Data visualizations (omics data, info graphics, complex data visualizations)

• Data management (raw data, project data, code repositories)

• Data transfer/submission from/to public repositories (GEO, SRA, EGA, ENA, etc.)

• Manuscript writing (methods, results, etc.)

• Support for grant and project proposal writing

• Bioinformatics workshops & seminars

• Supervision of students, internships

• Consultancy on all aspects of Bioinformatics (statistics, programming, workflows)

DATA ANALYSIS

Genomics

• Genotyping and variant calling from whole-exome sequencing (WES), whole genome sequencing WGS, amplicon sequencing, panel sequencing and SNP microarrays.

Transcriptomics

• Expression analysis from RNA-seq (polyA, totalRNA) and miRNA, mRNA microarrays, (incl. target prediction).

• Analysis of alternative splicing and transcriptome diversity from RNA-seq.

• Variant calling (e.g. RNA editing) from RNA-seq.

• Fusion gene detection from RNA-seq.

Epigenomics

• Analysis of 5mC and 5hmC DNA methylation by microarray (EPIC, mouse), or NGS (whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Methyl-seq).

• Chromatin and transcription factor binding analysis by ChIP-seq, ATAC-seq, Cut&Run.

Epitranscriptomics

• Analysis of RNA-Protein-binding by CLIP-seq (binding and motif prediction).

Single Cell Omics

• Single cell analysis by scRNAseq and scATAC-seq (10X Genomics).

• Immuno-profiling from BCR/TCR sequencing.