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Open Access Research article

Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum

Israel Barrantes146, Gernot Glockner235, Sonja Meyer46 and Wolfgang Marwan46*

Author Affiliations

1 International Max Planck Research School, Magdeburg, Germany

2 Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany

3 Institute for Biochemistry University of Cologne, Joseph-Stelzmann-Str. 52, Cologne, Germany

4 Max Planck Institute for Dynamics of Complex Technical Systems and Magdeburg Centre for Systems Biology (MaCS), Otto von Guericke University, Magdeburg, Germany

5 Berlin Center for Genomics in Biodiversity Research Leibniz Institute for Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, D-12587 Berlin, Germany

6 Magdeburg Centre for Systems Biology (MaCS), Otto von Guericke University, Sandtorstr. 1, D-39106 Magdeburg, Germany

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BMC Genomics 2010, 11:115  doi:10.1186/1471-2164-11-115

Published: 17 February 2010

Additional files

Additional file 1:

Figure S1. Overview of the Experimental Design. A summary of experiments and computational analyses is depicted. RNA samples were taken from competent plasmodia after six days of starvation in the dark, and from competent plasmodia at six hours after exposition to a 30 minutes pulse of red light (≥ 700 nm) (1) [3]. cDNAs were synthesized from extracted RNAs (2), and sequenced and quantitated using the 454 Life Sciences platform (3) [7,8]. Contigs generated were then annotated at every bioinformatic level (4), and network interactions (5) were obtained both by a combination of manual curation of literature, expression data, and predictions from annotations (Powerpoint file).

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Additional file 2:

Transcript Abundance Data. Hit counts obtained from pyrosequencing, including statistical analyses (Excel spreadsheet).

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Additional file 3:

Figure S2. Hits Distribution of Transcript Species. The distribution of pyrosequencing hit counts respect to the number of transcript species on each library (starvation and light-induced) is depicted on a semi-logarithmic scale. Hit counts are included in the adjacent upper ranges to the right; for example, transcripts with 2 hits are present in the 2-5 range. Similar distributions of contig species were found on both libraries, and most transcripts were represented by 1 to 5 hits only (Powerpoint file).

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Additional file 4:

Similarity Results. Results of the similarity analyses against protein databases from sequences with hit counts data (Excel spreadsheet).

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Additional file 5:

Table S1. Annotated transcripts with relative frequencies higher than 0.005. A list of transcripts obtained from the scatterplot of relative frequencies (Figure 1) is depicted. Annotations, hit counts, and probability values follow the same convention as in Table 2 (Word document).

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Additional file 6:

Table S2. Overrepresented Gene Ontology terms in Upregulated Transcripts. Full lists of GO terms from up- and downregulated contigs were compared against each other using the Fisher's exact test from the GOSSIP program [18], as implemented in BLAST2GO [16]. A two-tailed test with the false discovery rate (FDR) filter was employed. The number of GO-annotated transcripts used for comparison between up- (Test) and downregulated (Ref) groups of cDNAs is shown. All overrepresented GO terms belong to the biological process (BP) category (Word document).

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Additional file 7:

Transcriptome Annotation. Annotations of all sequences, including those with or without hit counts data (Excel spreadsheet).

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Additional file 8:

Table S3. Top 20 Transcripts Downregulated in Light-induced Plasmodia. Transcripts with the highest rates of downregulation (relD/relL > 1.0), are listed. BLAST2GO [15] automatic annotations were used, and manual corrections were included in some cases. Transcripts with unknown orthologs are described with "---NA---." Annotations, SwissProt accessions, hit counts, and probability values follow the same convention as in Table 2 (Word document).

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Additional file 9:

Table S4. Top 20 Transcripts Upregulated in Light-induced Plasmodia. Transcripts with the highest rates of upregulation (relL/relD > 1.0), are listed. BLAST2GO [15] automatic annotations were used, and manual corrections were included in some cases. Columns follow the same convention as in Table S3 (Word document).

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