Global analyses platform - Affymetrix Microarrays

Center of Excellence for Fluorescent Bioanalytics (KFB) - University of Regensburg, Regensburg, Germany

The Center of Excellence for Fluorescent Bioanalytics (KFB) is a leading Service Provider for Affymetrix microarray applications.  The service portfolio comprises the complete range of Affymetrix expression analysis products including the GeneTitan® technology, the latest type of plate based microarrays.  The lab is fully equipped and all current protocols are well established.  Quality and quantity of initial RNA and all intermediate products are routinely determined by microfluidics 'Lab-on-a-Chip' technology (Agilent 2100 Bioanalyzer) and UV-Vis spectrophotometer (Nanodrop ND-1000).

As a partner of TRANSVAC, KFB offers genome-wide expression analysis with Affymetrix GeneChip® Array Plates or Single Cartridge Microarrays. KFB will provide premium service along the full workflow of microarray projects, including advice in experimental design, sample handling and storage, RNA isolation from cells and tissues, sample processing, hybridisation, scanning, data acquisition, data analysis, and data storage. Rigorous QC monitoring and full documentation are in place for each step.

On-site access

The KFB will facilitate on-site access upon request by way of individual User trainings for two applicants for a maximum of three days. Basic knowledge in molecular biology techniques and biostatistics are required.

Modalities of access

Organisation short name: UREG                                           

Unit of access: one unit is equivalent to about 30 samples

Quantity of access available: The KFB will have the capacity for a maximum of 20 medium-sized projects throughout the entire duration of TRANSVAC. Depending on array type and processing protocol, a typical project may be comprised of up to 32/48 samples using GeneChip® Array Plates (16- or 24-well format) or 24 samples hybridised to GeneChip® single cartridge arrays. The KFB will be able to combine a low number of independent projects at once.

Timelines: two months per experiment

Overview of access provided between January 2011 (1st call) and April 2013 (10th call):
Min. quantity of access to be provided: 14
Estimated number of users/User groups: 14
Estimated number of projects: 14
Access already provided: 14
Access still available: 0

Last call submission date scheduled for: This service is only available via paid access. The application period for the call is now closed.

Input – sample requirements:

Due to the short timelines (end of TRANSVAC project: September 2013), special conditions are requested by the KFB for the eligibility of the applications to the AFFYMETRIX Microarrays service at the TNA1304-10 call.
The User should provide high-quality RNA samples (RIN 6 or higher; no carrier-RNA added) prepared at the User's site. The samples should be available for shipment when the outcome of the application review will be known (end of May 2013).
For each RNA the KFB will perform a quality control (Bionalyzer profile) and a quantity determination (Nanodrop UV-Vis spectrogram) prior to sample processing.
Processing protocols will be chosen based on the amount of samples the user is able to provide: standard Affymetrix protocol for RNA amounts ≥ 100 – 300 ng; small-sample protocol for total RNA amounts ≥ 500 pg.

Please note that the User should confirm in the application form that his/her Institution will be able to provide all necessary documentation (Material Transfer Agreement; safety documents, if applicable) within a maximum of three weeks after having been contacted by the Service provider (June 2013, after the outcome of the application review).

Output – deliverables to User:

All raw data, the QC report and the result files will be made available to the Users. Raw image files of single arrays (CEL files) will be provided to allow for alternative data analysis routines. Quality parameters of all experimental stages will be summarised in PDF or PNG format. The main result file (Excel format) will contain fully annotated data for all analyses performed.

Optional Services NOT included in the free access

Real-Time PCR validation of candidate genes and extended statistical as well as in-depth functional data analysis are not part of the standard free Transnational Access package, but can be performed on request.

Contact

Thomas Stempfl

thomas [dot] stempfl [at] exfor [dot] uni-regensburg [dot] de

+49 941 943 5011