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Open Access Research article

Organ-specific alterations in tobacco transcriptome caused by the PVX-derived P25 silencing suppressor transgene

Balaji Jada, Arto J Soitamo and Kirsi Lehto*

Author Affiliations

Department of Biochemistry and Food Chemistry, Laboratory of Molecular Plant Biology, University of Turku, Itäinen pitkäkatu 4B, 6. floor, PharmaCity, FI-20520, Finland

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BMC Plant Biology 2013, 13:8  doi:10.1186/1471-2229-13-8

Published: 8 January 2013

Additional files

Additional file 1:

Table S1. RT-qPCR results indicating the equal detection of the P25 transcript from the leaves, and the flowers of the three transgenic plants that were used in the microarray analysis.

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Additional file 2:

Table S2. Normalized microarray data showing the up-regulated transcripts in leaves of P25 expressing plants.

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Additional file 3:

Table S3. Overview of the up-regulated transcripts detected in the leaves of the P25 expressing plants.

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Additional file 4:

Table S4. Normalized microarray data showing the up- and down-regulated transcripts in flowers of P25 expressing plants.

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Additional file 5:

Table S5. Overview of the up-and-down regulated transcripts detected in the flowers of the P25 expressing plants.

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Additional file 6:

Table S6. Up-regulated transcripts related to the protein synthesis and proteolysis in leaves of P25 expressing plants.

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Additional file 7:

Figure S1. Up-regulation of signaling related genes (log2 value >1) is shown by using the MapMan software. The blue squares represent the number of genes up-regulated in different pathways that are involved in signaling.

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Additional file 8:

Figure S2. 2D-polyacrylamide gel electrophoresis (2D-PAGE) analyses of the proteins separated from four separate sets of wild type (left panels) and P25-expressing transgenic plants (right panels) to visualize levels of various individual proteins. Gels are stained using coomassie blue. The molecular weight markers (loaded on the right side of the gels in the two upper panels, and on the left side of the gels in the two lower panels) represent weights of 250, 130, 100, 70, 55, 35, 25, 15 and 10 kDa. Equal amounts (250 μg) of the solubilized leaf protein samples were initially loaded to ach of the isoelectric focusing runs. Equal loadings were confirmed by 1D-SDS-PAGE gels (data not shown).

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Additional file 9:

Table S7. List of genes that are up-regulated in leaves of all the P25, AC2 or HC-Pro VSRS expressing transgenic plants, as detected by microarray [21,49].

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Additional file 10:

Table S8. Overview of the transcripts that are up-regulated in all the P25, HC-Pro and AC2 VSRS expressing transgenic plants, as detected by microarray analysis [21,49].

Format: DOCX Size: 17KB Download file

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Additional file 11:

Figure S3. Over-presentation analysis using PageMan of leaves expressing P25, HC-Pro or AC2. The test was performed using Fisher’s exact test including FDR <0.05.

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Additional file 12:

Table S9. RT-qPCR conditions and the sequences of the primers that were used to validate the microarray data.

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