Research article
Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development
-
* Corresponding author: Grant R Cramer cramer@unr.edu
1 Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557-0014, USA
2 Department of Animal Biotechnology, University of Nevada, Reno, NV 89557-0014, USA
3 Boston University School of Medicine, Department of Genetics and Genomics, Boston University, E632, Boston, MA 02118, USA
BMC Genomics 2007, 8:429 doi:10.1186/1471-2164-8-429
Published: 22 November 2007Additional files
Additional file 1:
Quality control of Vitis GeneChip® genome arrays. The data provided represent the quality controls and commercial specifications of the 21 arrays used in this study. Slide 1. A) Box plot of raw PM (perfect match) probe intensities before and after RMA normalization. Each color indicates a set of three biological replicates. B) RNA degradation plot for all 21 arrays. All lines have similar shapes and similar variation between highest and lowest points. C) Commercial specifications of the Affymetrix Vitis GeneChip® version 1.0.
Format: PPT Size: 420KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 2:
Extensive list of transcripts differentially expressed along berry development. The data provided represent the lists of transcripts that fulfilled the ANOVA filter. Table 1: List of probe sets that passed the ANOVA filter. Table 2: List of Unigenes that passed the ANOVA filter. Table 3: List of probe sets that passed the two-fold ratio (TFR) or greater filter for transcript abundance changes between two stages over berry development. Table 4: List of Unigenes according to Profile number that passed the two-fold ratio (TFR) or greater filter for transcript abundance changes between two stages over berry development.
Format: XLS Size: 7.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 3:
Principal component analysis of transcriptomic behavior during grape berry development. Hybridization data from each biological replicate were projected as two graphs according to the A) first and second and B) second and third principal components arranged in descending order of variance. These first three principal components allowed clear distinction of the seven developmental stages with spots representing data from each biological replicate: E-L stage 31 (light green), 32 (dark green), 33 (brown), 34 (burgundy), 35 (yellow), 36 (light purple), and 38 (orange). Analysis was performed using GeneANOVA software [118].
Format: PPT Size: 599KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 4:
Template profiles used for PTM analysis. The data provided represent the schematic trends of transcript profiles across berry development used for defining the template profiles. Phases are indicated as I, II, or III. Numbers indicated E-L stages 31 to 38. Pink shading indicates véraison (E-L stages 34 to 35).
Format: PPT Size: 135KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional file 5:
Supplemental data related to the functional analyses of the Unigenes and to real-time RT-PCR. The data provided represent supplemental data related to Figures 3 and 10. Table 1. Attribution of the 20 profiles to Phase I, II or III according to criteria cited in Methods. Table 2. p-values of the Chi-squared tests of distribution of Unigenes within the three main phases of berry development (I, II and III) for each functional category. Differences in distribution considered as significant are indicated by orange shading. Only Unigenes clustered into the 20 PTM profiles were used for this analysis. Table 3. A list of primers used for quantitative real-time RT-PCR experiments.
Format: DOC Size: 115KB Download file
This file can be viewed with: Microsoft Word Viewer