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Open Access Research article

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

Amit Sinha1, Ralf J Sommer1* and Christoph Dieterich2*

Author Affiliations

1 Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, 72076, Tübingen, Germany

2 Berlin Institute for Medical Systems Biology (BIMSB) at the Max Delbrück Center for Molecular Medicine Berlin, Robert-Röβle-Str. 10, 13125, Berlin, Germany

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BMC Genomics 2012, 13:254  doi:10.1186/1471-2164-13-254

Published: 19 June 2012

Additional files

Additional file 1:

Figure S1.The impact of different normalization strategies on expression fold change estimation. a) The general concept of using spike-ins to control for changes in total mRNA abundance relative to total RNA. See van de Peppel et al., 2003 for a detailed explanation. b) MA-plot of a Loess based normalization assuming a net mRNA expression fold change of 0 between the two samples. The M axis depicts the log2 fold change between the red and green microarray channels. The A axis is the average log2 intensity across both microarray channels. The position of the spike-in signals (colored dots) clearly indicate a deviation from this assumption. The corresponding legend in the upper left shows the expected fold change of the spike-ins relative to total RNA levels. Consequently, the location of the spike-ins corresponds to a down-shift of mRNA abundance levels within the total RNA population. c) Differentially expressed gene counts for the dauer vs. mixed stage comparison conditional on the normalization strategy. Figure S2. Explanation of a common reference design for microarrays (see Eisen and Brown 1999). For each species, RNA from biological replicates of mix-stage worms (M1 to M4) were combined together to generate one common reference pool. Labelled aRNA produced from independent biological replicates were then co-hybridized with labelled aRNA from the common reference pool, including two dye-swaps. Samples D1 to D4 represent Dauer samples and DE1 to DE4 represent dauer exit samples at 12 hour timepoint. The blue arrows indicate the direction of labelling in each co-hybridization (arrow head = Cy3 labelled, arrow tail = Cy5 labelled). This design allows comparison via the common reference pool, but at the same time remains flexible for adding more time-points to the study, if needed. Figure S3. Cumulative plot of log2 expression fold changes for genes with and without sequence conservation (pioneer genes). The two distributions are significantly different (two-sample Kolmogorov-Smirnov test; p-value < 10E- 16).

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Additional file 2:

Table S1. Differential expressed genes in the dauer versus dauer-exit comparison inP. pacificus.

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Additional file 3:

Table S2. Differential expressed genes in the dauer versus dauer-exit comparison inC. elegans.

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Additional file 4:

Table S3. Differential expression ofP. pacificuscellulase genes that were acquired by horizontal gene transfer. Table S4. Differential expression of P. pacificus diapausin genes that were acquired by horizontal gene transfer.

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