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Impact of RNA degradation on gene expression profiling

Lennart Opitz1, Gabriela Salinas-Riester1, Marian Grade2, Klaus Jung3, Peter Jo2, Georg Emons2, B Michael Ghadimi2, Tim Beißbarth3* and Jochen Gaedcke2

Author Affiliations

1 DNA Microarray Facility, University Medicine Göttingen, Humboldtallee 23, 37073 Göttingen, Germany

2 Department Surgery, University Medicine Göttingen, Robert-Koch-Str. 40, 37073 Göttingen, Germany

3 Department Medical Statistics, University Medicine Göttingen, Humboldtallee 32, 37073 Göttingen, Germany

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BMC Medical Genomics 2010, 3:36  doi:10.1186/1755-8794-3-36

Published: 9 August 2010

Additional files

Additional file 1:

Supplementary Figure S1. The absolute distance of the probe to the cDNA 3' end for all genes from the following groups is shown: normally-represented, under-represented and over-represented genes in TP3 vs Control. The numbers on top indicate the significance levels. The p-values were obtained using the two-sample Wilcoxon test and are Bonferroni corrected. The numbers at the bottom indicate the quantity of genes belonging to the respective group.

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Additional file 2:

Supplementary Figure S2. We checked the technical reproducibility of Agilent microarray results using the 3 patient samples analyzed here. We investigated the robustness of gene expression profiles in dependence of: 1. the experimenter (E); or 2. repeating the labelling (L); or 3. repeating the hybridization (H); or 4. using different washing methods (W). These types of technical replicates where highly correlated and clustered together. Supplementary Figure 2 shows pairwise correlations between all samples of patients. The elements of the matrix in the visualization are colored by Pearson's correlation coefficient values with deeper colors indicating higher positive (blue) correlations. The heatmap is flanked by clustering dendrograms showing the similarity between samples in a hierarchical approach.

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