Open Access Highly Accessed Methodology article

RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization

Tomas Hruz2, Markus Wyss2, Mylene Docquier3, Michael W Pfaffl4, Sabine Masanetz4, Lorenzo Borghi1, Phebe Verbrugghe6, Luba Kalaydjieva6, Stefan Bleuler5, Oliver Laule5, Patrick Descombes3, Wilhelm Gruissem1 and Philip Zimmermann1*

Author Affiliations

1 Department of Biology, ETH Zurich, 8092 Zurich, Switzerland

2 Institute of Theoretical Computer Science, ETH Zurich, 8092 Zurich, Switzerland

3 Genomics Platform, NCCR 'Frontiers in Genetics', University of Geneva, 1211 Geneva 4, Switzerland

4 Physiology Weihenstephan, TUM, Weihenstephaner Berg 3, 85354 Freising, Germany

5 NEBION AG, Hohlstrasse 515, 8048 Zurich, Switzerland

6 Western Australian Institute for Medical Research, UWA Centre for Medical Research, Perth, Australia

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BMC Genomics 2011, 12:156  doi:10.1186/1471-2164-12-156

Published: 21 March 2011

Additional files

Additional file 1:

List of publications related to reference gene validation. Publications that report about the validation of small sets of commonly used reference genes for various biological contexts.

Format: PDF Size: 77KB Download file

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Open Data

Additional file 2:

Variance of gene expression across different array types. Standard deviation of signal intensity versus mean signal intensity for all probe sets from different Affymetrix array types available in Genevestigator.

Format: PDF Size: 847KB Download file

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Additional file 3:

Variance of gene expression across different tissue types. Standard deviation of the top 50 probe sets that were most stable across all conditions (5014 samples from the AffymetrixHuman133 2.0 platform) across 186 different tissue categories.

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Additional file 4:

Ranking of the SD of the most stable probe sets across different mouse tissues. Ranking of the SD of the most stable probe sets identified for a variety of mouse tissue samples (AffymetrixMouse430 2.0 platform).

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Additional file 5:

Ranks of the SD of commonly used reference genes across different mouse tissues. Ranks of the SD across different tissues of probe sets representing commonly used reference genes in mouse (AffymetrixMouse430 2.0 platform).

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Open Data

Additional file 6:

GeNorm calculations. This figure shows the complete set of GeNorm calculations for the results summarized in Figure 3 of the article.

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Additional file 7:

Original measurement data of RT-qPCR validation experiments. For each validation experiment, the original Cq values for each sample are provided.

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Additional file 8:

Pre-validation of reference genes for CD4 T-lymphocytes. This figure shows screen shots of meta-profile data for candidate reference genes for CD4 T-lymphocytes.

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