Transcription Profiling of Signal Transduction


Supplemental Tables

 

Table S-I - Expression patterns of the SUCAST chip components in leaves of different individuals. M=log2 rat io of the microarray signal intensity between the experimental sample and the reference (pool), LV=leaf. The numbers 1 and 2 and the letters a, b and c denote the differe nt biological samples.


Table S-II - Expression patterns of the SUCAST chip components. The table indexes the log2 ratios of the mi croarray signal between the two channels (Cy3 and Cy5). For each clone, the median intensity value of the technical replicates was used to calculate the ratio between the experimental samples and the reference sample. M=log2 ratio of the microarray signal intensity. FL=flower, LB=lateral bud, LV=leaf, RT=root, IN1=internode 1, IN4=interno de 4. The numbers 1 and 2 denote the different biological samples of each tissue. * indicates that the SAS identity was not confirmed by re-sequencing.


Table S-III - Replicate data consistency an distribution in relation to the cut-off limits. i=image; p.down= percentage of points below the cut-off limits; p.up=percentage of points above the cut-off limits; p.inside=percentage of points inside the cut-off limits; down=number of replicate points below the cut-off limits; up=number of replicate points above the cut-off limits; inside=number of replicate points inside the cut-off limits; total=tot al number of replicate points obtained; median=log2 of the intensity ratios between the two microarray channels; mad=median absolute deviation of the retios among the tec hnical replicates.


Table S-IV - Sugarcane genes selected for real-time PCR validation, primers designed and entropy (H) values. Di fferentially expressed genes and genes with ubiquitous expression profiles were selected for the validation protocol. The polyubiquitin and the 14-3-3 genes (marked with an asterisk) were used as references for normalization. The tubulin and the actin genes were also tested as references. BLAST searches against the SUCEST database were co nducted to ensure the specificity of the selected primers. The values of entropy shown were calculated using the polyubiquitin gene as the reference. Similar results were obtained using the 14-3-3 gene (data not shown). For a description of the entropy calculation, refer to the Methods section. The H values are also exemplified for the re ference genes. The H value shown for the polyubiquitin gene was calculated using the 14-3-3 gene as a reference for normalization.


Table S-V - SUCAST catalogue. Catalogued sugarcane signal transduction components.


Table S-VI - SUCAST components with ubiquitous expression patterns. The table indexes all genes that did not show preferential expression in any of the tissue samples (i.e., with more than 55% of the replicate data points inside the cut-off limits in all samples analyzed). * indicates that the SAS identity was not confirmed by re-sequencing.


Table S-VII - SUCAST expression profile matrix. Normalized microarray signal intensity values were used to calculate SUCAST gene expression ratios among twelve different samples of six sugarcane tissues. Pairwise comparisons provided a portrait of the spatial distribution of each transcript analyzed. The six last columns of the matrix contain the ratio obtained from the hybridizations of each tissue sample against the reference sample (pool of tissues).