Research article
Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus
-
* Corresponding author: Mark L Blaxter mark.blaxter@ed.ac.uk
- † Equal contributors
1 Cardiff School of Biosciences, BIOSI 1, University of Cardiff, P.O. Box 915, Cardiff, CF10 3TL, UK
2 Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3JT, UK
3 Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire, PE28 2LS, UK
4 Microarray Department and Integrative Bioinformatics Unit, Faculty of Science, University of Amsterdam, Kruislaan 318, Building I, Room 105C, 1098 SM Amsterdam, The Netherlands
5 School of Biomedical and Health Sciences, Pharmaceutical Sciences Division, Franklin Wilkins Building 150, Stamford St., London, SE1 9NH, UK
BMC Genomics 2008, 9:266 doi:10.1186/1471-2164-9-266
Published: 3 June 2008Additional files
Additional File 1:
Table showing cDNA libraries sampled for expressed sequence tags. A summary of the cDNA libraries constructed and sampled for the project.
Format: DOC Size: 62KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional File 2:
Sequences of oligonucleotides forming the reference probe. This table gives the sequences of the oligonucleotides used as a reference probe for the microarray hybridisation experiments.
Format: DOC Size: 38KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional File 3:
Assessment of micro-array sensitivity and signal linearity. Representative analysis of the fluorescent signal generated by 10 RNAs introduced at known concentrations prior to labelling and detected by complementary reporter (10 replicates of each reporter spotted on the array). Panel A are data generated from Cadmium control array replicate 4, panel B is from Fluoranthene control replicate 7 and panel C is from Atrazine control replicate 1. The average signal is indicted by closed circles with technical error bars representing the standard error of the measurements. A fitted regression line is shown for the linear portion of the response together with the R2 value for the fitted line.
Format: PPT Size: 1.8MB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional File 4:
Distribution of array micro-array data post normalisation. The distribution of the normalised data is shown for samples employed for analysing transcript changes in response to developmental stage (Panel A), together with Cadmium (Panel B) fluoranthene (Panel C), and Atrazine (Panel D) exposure. Boxes are waisted at the distribution median and encompass the interquartile range, with whiskers indicating a further 1.5× the interquartile distance.
Format: PPT Size: 989KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional File 5:
Graphical representations of relative gene expression against fluorescence intensity from control and xenobiotic-exposed samples. Array data were normalised and filtered (as described in Materials and Methods) and the log2 of the average fold change (M) plotted against the log2 of the average mean signal intensity (A). Panel A shows a MA plot for control earthworms from the Cadmium exposure experiment whilst Panel B displays data from organisms exposed to 500 ppm Cadmium. Metallothionein ESTs are highlighted within the dashed circle.
Format: PPT Size: 1.8MB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional File 6:
Transcripts significantly changed between adult and juvenile earthworms. A table showing all transcripts identified as changing significantly between adult and juvenile earthworms (T-test, p < 0.01, Bonferroni False Discovery Rate)
Format: XLS Size: 225KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 7:
Transcripts significantly changed in adult earthworms exposed to cadmium. A table showing all transcripts identified as changing significantly in adult earthworms exposed to cadmium (ANOVA, p < 0.05, Benjamini and Hochberg False Discovery Rate)
Format: XLS Size: 86KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 8:
Transcripts significantly changed in adult earthworms exposed to fluoranthene. A table showing all transcripts identified as changing significantly in adult earthworms exposed to fluoranthene (ANOVA, p < 0.05, Benjamini and Hochberg False Discovery Rate)
Format: XLS Size: 350KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 9:
Transcripts significantly changed in adult earthworms exposed to atrazine. A table showing all transcripts identified as changing significantly in adult earthworms exposed to atrazine (ANOVA, p < 0.05, Benjamini and Hochberg False Discovery Rate)
Format: XLS Size: 73KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 10:
Functional Transcript Clusters Significantly (p < 0.05) Changed During Cadmium Exposure of Adult Earthworms. A table showing the functional identifications of transcripts showing altered abundance following cadmium exposure.
Format: XLS Size: 21KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 11:
Functional Transcript Clusters Significantly (p < 0.05) Changed During Fluoranthene Exposure of Adult Earthworms. A table showing the functional identifications of transcripts showing altered abundance following fluoranthene exposure.
Format: XLS Size: 22KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 12:
Functional Transcript Clusters Significantly (p < 0.05) Changed During Atrazine Exposure of Adult Earthworms. A table showing the functional identifications of transcripts showing altered abundance following atrazine exposure
Format: XLS Size: 29KB Download file
This file can be viewed with: Microsoft Excel Viewer