Online Supplement for Szakasits et al. (2008)

These pages contain supplementary material for the manuscript.

The Transcriptome of Syncytia Induced by the Cyst Nematode Heterodera schachtii in Arabidopsis Roots

Dagmar Szakasits,¹ Petra Heinen,¹ Krzysztof Wieczorek,¹ Julia Hofmann,¹ Florian Wagner,² David P. Kreil,³ Peter Sykacek,³ Florian M. W. Grundler¹ Holger Bohlmann,¹

1. Institute of Plant Protection, Department of Applied Plant Sciences and Plant Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
2. RZPD, Germany; present address: ATLAS Biolabs GmbH, Berlin, Germany
3. WWTF Chair of Bioinformatics, Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria

Add link to original journal article once published.

These pages provide a comprehensive archive of supplementary data and results for the above journal manuscript. The tables comprise thousands of pages and are provided so that readers can easily search for particular genes in the list of results.

This page lists content sorted by type and in the context of a short description. To complement this, for easier reference by figure and table number (following the order of appearance in the manuscript text), please use the below links:

• Table 1: Syncytium vs Root, all
• Table 2: Syncytium vs Root, strongly up
• Table 3: Syncytium vs Root, strongly down
• Table 4: Contingency tables (on this page)
• Table 5: Highly expressed genes in Syncytia
• Table 6: 15 dpi vs 5 dpi Syncytium, up/down
• Table 7: 15 dpi vs 5 dpi Syncytium, all
• Table 8: Gene Ontology tables (on this page)
• Table 9: Genevestigator
• Supplementary Figure 1: Syncytium vs Root, M(A))
• Supplementary Figure 2: 15 dpi vs 5 dpi Syncytium, M(A)

Appendix S1: Methods

We provide supplementary documents providing further details on the microarray experiments and data analysis methods employed as well as particulars about the performed quantitative real-time and in situ PCR.

Appendix S2: Archive of data and sample description tables

• An archive containing the raw CEL data for the 11 hybridizations analysed in the paper will be made available here from the publication date.  [ 37.3MB zip ]
• We provide an extensive description of the performed sample measurements through a table of target meta data (one row per sample).
• After normalization and weighted summarization using reannotated probesets as detailed in the Methods section we obtained the normalized transcript signals on log₂-equivalent scale underlying subsequent statistical analysis.  [ 3.3MB zip ]

Appendix S3: Low-level microarray analysis and diagnostic plots

Diagnostic plots are provided of the raw, unnormalized data. These have been used to determine an appropriate normalization method. Subsequent diagnostics verify successful normalization and examine data set characteristics for systematic trends and artefacts.

• Traditional M(A) plots for all pairs of chips showing the need for normalization after probe sequence specific background subtraction. Some summary statistics are included in panels below the diagonal. Coloured curves track a loess fit of M(A).  [ 8.1MB pdf ]
• Exploratory scatter plots (panels above diagonal) and quantile-quantile plots (panels below diagonal), both after probe sequence specific background subtraction. The lack of systematic trends in the quantile-quantile plots mapping to biological classes indicates the suitability of quantile-quantile normalization for this data set.  [ 11.2MB pdf ]
• Residuals in a robust fit of a linear probe level model after probe sequence specific background subtraction and quantile-quantile normalization. These show some random spatial artefacts, which have been dealt with by appropriate downweighting of the affected probes in a robust iterative weighted least squares fit in the probe signal summarization process.  [ 23.9MB pdf ]

Analysis results

• Main contrasts in a batch detrending linear model are listed in the comprehensive tables below.

  [Supplementary Table 1] Contrast: Syncytium vs Root. Listing differential expression for all genes.   [ 5.0MB pdf ]
  Subsets of this table showing differential expression for a multiple-testing corrected FDR<5% are available as Supplementary Table 2 (upregulation) and Supplementary Table 3 (downregulation).

  [Supplementary Table 7] Contrast: 15 dpi Syncytium vs 5 dpi Syncytium. Listing differential expression for all genes.   [ 4.3MB pdf ]
  A subset of this table showing differential expression for a multiple-testing corrected FDR<5% is available as Supplementary Table 6, showing (a) upregulated and (b) downregulated genes.

• [Supplementary Table 5] The 10% most highly expressed genes in Syncytia.   [ 490kB pdf ]
• [Supplementary Table 4] Contingency Tables for Fisher's Exact test.

  (a) Contingency tables and Fisher's Exact test for the overrepresentation of peroxidase genes in downregulated transcripts.

  (b) Contingency tables and Fisher's Exact test for the overrepresentation of MIPS genes in downregulated transcripts.

• [Supplementary Table 8] Gene Ontology Analysis Results.

  (a) GO categories preferentially upregulated.

  (b) GO categories preferentially downregulated.

  Tables are tab-delimited and are easily viewed in all popular spreadsheet programs.

• [Supplementary Table 9] Genevestigator table. Expression of the 100 strongest upregulated genes according to Genevestigator.
• M(A) plots for main contrasts including standard errors (grey bars).

  [Supplementary Figure 1] Contrast: Syncytium vs Root. See Table S1 for a full list of gene names (5.0 MB pdf).   [ 824kB pdf ]

  [Supplementary Figure 2] Contrast: 15 dpi Syncytium vs 5 dpi Syncytium.   [ 814kB pdf ]