The Medical Bioinformatics Centre (MBC) provides basic and advanced bioinformatics support for the analysis of high-throughput data produced by modern biotechnologies, including genomics, transcriptomics, epigenomics, proteomics, metagenomics and metaproteomics. The support is targeted for researchers based in Finnish research institutions but is also available for international academic researchers and non-academic users. In addition, extensive collaborative development projects are possible for a limited number of scientifically outstanding projects.

The projects are selected based on their feasibility given our available resources. The analysis time depends on the data and resources and hence, working time schedule and working costs will be estimated separately for each project.

An experimental study design consultation meeting is included in all of our support tracks. In this meeting, the bioinformatics and statistics aspects of the project are discussed. It is important for us to understand the scientific problem and the goal of the project. The earlier this meeting can be arranged in the course of the project (optimally before performing the biological experiments), the better it ensures that the scientific problem is addressed the best possible way in terms of the data analysis. The data are analyzed using robust standard tools and/or in-house tools depending on the nature of the project. A comprehensive report describing the analysis methods and parameters is provided for all projects.

MBC personnel contributing with their scientific knowledge to solve scientific questions are to be acknowledged as co-author(s) in the resulting scientific publications, in line with the ICMJE Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals. Separate project agreement is made with each collaborator, specifying also the authorships. By applying for MBC Support you also agree to our User Agreement.

Please, make a request for the bioinformatics support by filling our
button for the support request form

Basic support

Basic analysis support for transcriptomics:

The support covers mRNA sequencing data produced using Illumina sequencing technology.

The basic analysis includes the following steps:

  1. Quality control of raw reads
  2. Mapping of reads to reference (human or mouse) and quality control of the mapped reads
  3. Normalization and data quality overview
  4. Expression quantification at the gene level
  5. Statistical testing for differential expression in comparisons between two groups of samples
  6. Filtering of differentially expressed genes using default thresholds (false-discovery-rate<0.05 and absolute fold-change>2)

Basic analysis support  for Chromium 10x single cell RNA sequencing:

The basic analysis includes the following steps:

  1. Quality control of raw reads
  2. Mapping of read to reference genome (human or mouse) and quality control of the mapped reads
  3. Division of reads to cells
  4. Generation of gene expression (feature-barcode) matrices
  5. Preliminary clustering of cells based on their expression profiles
  6. Production of input files for Loupe cell browser

Advanced support

Collaboration-based data analysis support is available for large and complex projects requiring non-standard analysis setups, where the typical amount of bioinformatics work is 1-2 months. For example the following data types are frequently processed:

  • RNA sequencing
  • DNA sequencing
  • ChIP sequencing (transcription factors, histone modifications)
  • ATAC sequencing
  • RRBS (reduced representation bisulfite sequencing)
  • Single cell RNA sequencing
  • Metaproteomics
  • Metagenomics (16S rRNA gene sequencing, shotgun metagenomics)
  • Proteomics
  • Clinical data

Collaborative development projects

Extensive bioinformatics collaboration is available for a limited number of scientifically outstanding projects, where a tailored data analysis workflow and/or method development is required. Typically the amount of bioinformatics work in these projects is more than three months.
With extensive bioinformatics needs we recommend you to contact us at the stage when you are planning to apply funding for your project.