Online Supplement for Siddique et al. (2008)

These pages contain supplementary material for the manuscript.

Myo-Inositol Oxygenase Genes are Involved in the Development of Syncytia Induced by Heterodera schachtii in Arabidopsis Roots

Shahid Siddique,¹ Stefanie Endres,² Jamie M. Atkins,³ Dagmar Szakasits,¹ Krzysztof Wieczorek,¹ Julia Hofmann,¹ Claudia Blaukopf,¹ Peter E. Urwin,³ Raimund Tenhaken,² Florian M. W. Grundler,¹ David P. Kreil,⁴ Holger Bohlmann¹

1. Institute of Plant Protection, Department of Applied Plant Sciences and Plant Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
2. University of Salzburg, Plant Physiology, Hellbrunnerstr. 34, A-5020 Salzburg, Austria
3. Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, U.K.
4. 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.

Methods

We provide a supplementary document providing further details on the microarray experiments and data analysis methods employed.

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 ]

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

Tables / results specific to MIOX genes

• [Supplementary Table 1] Normalized gene expression data table for display or data table for download for the 71 selected genes involved in UDP-GlcA and myo-inositol metabolism. Each column holds the normalized log₂ signal intensity for an array. The column headers show the array name, with each column corresponding to a row in the table of target meta data.
• [Supplementary Table 2] Genevestigator table. Relative expression pattern of MIOX, UGD and USP in different organs of Arabidopsis according to Genevestigator.
• [Supplementary Table 3] Overview table of MIOX transcript expression in syncytia induced by H. glycines in soybean.
• M(A) plots for main contrasts including standard errors (grey bars).

  [Supplementary Figure 1] Contrast: Syncytium vs Root.

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

• Micrograph gallery

  [Supplementary Figure 3] MIOX4::GUS expression in uninfected Arabidopsis lines.

  [Supplementary Figure 4] MIOX5::GUS expression in uninfected Arabidopsis lines.

  [Supplementary Figure 5] Anatomy of root sections of wild-type and double mutants.

Full tables / results for browsing

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

  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 for upregulation and downregulation.

  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 for upregulated and downregulated genes.

• The 10% most highly expressed genes in Syncytia.   [ 490kB pdf ]
• M(A) plots for main contrasts including standard errors (grey bars).

  Contrast: Syncytium vs Root. See table for a full list of gene names (5.0 MB pdf).   [ 824kB pdf ]

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