Open Access Highly Accessed Research article

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression

Sebastian Müller1, Clara Baldin2,3, Marco Groth4, Reinhard Guthke1, Olaf Kniemeyer2,3,5, Axel A Brakhage2,3 and Vito Valiante2*

1 Department of Systems Biology / Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, Jena 07745, Germany

2 Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, Jena 07745, Germany

3 Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, Jena 07745, Germany

4 Department of Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11a, Jena 07745, Germany

5 Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), Jena 07747, Germany

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BMC Genomics 2012, 13:519 doi:10.1186/1471-2164-13-519

Published: 2 October 2012

Additional files

Additional file 1:

Tables.xls (Excel file which includes all the cited supplementary tables).

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Additional file 2:

Figure S1. Length distribution of untranslated regions (UTRs). The analysis was based on 9912 3' and 5' UTR sequences. The red vertical lines indicate the average median length of the 5'UTRs (308) and the 3'UTRs.

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Additional file 3:

Figure S2. Comparison of delta_delta_Ct values obtained by qRT-PCR analysis (see also Additional file 1: Table S9). Values obtained by qRT-PCR analysis where compared to log2 fold changes (wt vs ΔmpkA) obtained by microarrays and mRNA-Seq based on 14 genes. Both technologies seem to agree with the qRT-PCR-data with an average Pearson correlation of r = 0.75 for microarrays and 0.55 for mRNA-Seq (Spearman correlation coefficient rs in brackets).

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Additional file 4:

Figure S4. 2D gel electrophoresis of protein extracts. Total proteins were extracted from A. fumigatus wild type (Cy5, green) and ΔmpkA mutant strain (Cy3, purple). Proteins were stained with the difference in gel electrophoresis (DIGE) labelling technique. Total proteins were separated in a pH gradient of 3–11 (nonlinear).

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Additional file 5:

Figure S3. Pair-wise scatterplot of all three technologies. Comparison of three different technologies that is 2D-DIGE proteomic, mRNA-Seq and microarray, to detect differentially expressed genes and proteins between the Δmpka strain and wild-type strain, based on log fold changes of 94 entries. The overall correlation was found to be low, especially between mRNA-Seq and proteomic, whereas the correlation between proteomic and microarray was higher.

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