Global analyses platform - Agilent Microarrays

Max Planck Institute for Infection Biology - Agilent platform, Berlin, Germany

The Core Facility Microarray (CFM) of the Max Planck Institute for Infection Biology (MPIIB) is equipped with all necessary microarray processing hardware and software required for transcriptomic and genomic profiling, including an ozone-free room. MPIIB CFM supplies support, expert knowledge, guidance and help in microarray experiments, starting with chip design, experimental setup, wet-lab realisation of experiments, data acquisition, up to data analysis and interpretation of the results. The equipment is either used by own personel or in cooperation with individual researchers or research groups. Different microarray platforms and labelling protocols are used at the CFM.

The infrastructure of the core unit allows a flexible design of commercial-custom microarrays as 'in situ' long-mer oligonucleotide microarrays produced from Agilent Technologies. Quality Control (QC) and quantification of RNA and DNA is analysed by microfluidics 'Lab-on-a-Chip' technology (Agilent 2100 Bioanalyser), while labeling efficiency is verified by UV-Vis spectrophotometer (Nanodrop ND-1000). Microarray analyses can either be realised as single-color or dual-color experiments. Image acquisition of hybridised microarrays is carried out by a high-resolution DNA microarray scanner (G2565BA, Agilent Technologies). Several software packages for image analysis and processing (Feature Extraction, Agilent Technologies), a highly scalable server-client-based data analysis platform (Rosetta Resolver) and pathway analysis software package (IPA, Ingenuity Systems) are established and used by the CFM.

As a partner of TRANSVAC, MPIIB CFM offers genome-wide expression analysis with Agilent microarrays. MPIIB CFM task will include, dependent on the demands, custom microarray design, experimental setup, RNA sample preparation, sample amplification, sample labeling, sample hybridisation, microarray washing and scanning, feature extraction, data analysis, interpretation of the results and QC measurements at all experimental stages.

On-site access

Upon request, onsite access to the MPIIB CFM may be granted as:

  • Individual user training for six applicants for up to five days in maximum.
  • Practical microarray course for a group of five trainees for three days maximum.

Experience in molecular biology techniques and basic knowledge in statistics will be mandatory for qualification.

Modalities of access

Organisation short name: MPIIB

Unit of access: 50 samples with single-color og 70 samples with dual-color.

Quantity of access available: This service is only available via paid access. Funding capacity for free services is exhausted.

Overview of access provided between January 2011 (1st call) and July 2012 (7th call):
Min. quantity of access to be provided: 12
Estimated number of users/User groups: 12
Estimated number of projects: 12
Access already provided: 14
Access still available: 0

Last call submission date scheduled for: This service is only available via paid access. Funding capacity for free services is exhausted.

Input – sample requirements:

Dependent on the biological safety level and the nature of the experiments the MPIIB CFM has different prerequisites for sample acceptance. In general, the MPIIB CFM will accept and process samples in Trizol, PAXgene, Tempus tubes or RNA preparations done at the User’s site. RNA samples prepared at the User site will require analysis of RNA integrity (Bioanalyzer) by the User and examination of the profiles by MPIIB CFM. Nevertheless, independent of the nature and composition of the biological material, an aliquot of the same sample or preparation should be retained at the User’s institute.

Output – deliverables to User:

The MPIIB CFM will deliver the analysed data, all QC measurements and reports in Excel format or PDF documents. Unprocessed scan files in TIF format and MAGE-ML or text based raw data files for second party data analysis will be provided.


Hans-Joachim Mollenkopf

mollenkopf [at] mpiib-berlin [dot] mpg [dot] de

+49 30 28460482