Additional File 1:

Microarray expression ratios for all probes significantly responsive to NaCl, and comparisons to previously published data. Probes are shown which, after one or more of the three time points following 150 mM NaCl treatment, (i.e. 6 h, 24 h, or 48 h), had a fold change in expression ratio (treated:control) that different significantly from 0 (log₂), according to SAM analysis (FDR < 5%) [21]. All probes were also filtered to remove those with low signal in both channels of more than 1/3 of the arrays at each time point, as described in Methods. Blank cells indicate that data has been removed due to filtering. Only probes with associated AGI identifiers are shown, and some AGI loci are represented by more than one probe. The expression ratios (log₂, treated:control) for each of 18 hybridizations (3 biological replicates by 2 dye-reversal replicates at each of the 3 time points) are shown in columns 5–22, and can be distinguished by the column headers. The mean expression ratio at each time point is given in log₂ scale in columns 23–25. Rows are sorted in decreasing order, according to the mean of all expression ratios in each row as shown in column 26. Microarray expression data was extracted from selected previous publications, and is summarized in columns 27–39, wherever genes common AGI numbers could be identified. All quantitative data is expressed as (log₂, treated:control) expression ratios. Columns 27–28 show expression ratios for all transcripts present on Affymetrix ATH1 arrays hybridized to 150 mM NaCl treated roots (6 h, 24 h), as described in the unpublished AtGenExpress data set prepared by the Kudla group [15]. Columns 29–30 show expression ratios only for up-regulated genes identified in NaCl treated roots (3 h, 27 h) measured on the 8,100 gene Affymetrix GeneChip, as described in Supplemental Table 1 of data prepared by Kreps and colleagues [12]. Column 31 shows expression ratios for genes identified as being up-regulated in roots after 2 h of 250 mM NaCl treatment, as reported in Table 2 of a report by Taji et al. [10]. These, as well as other relevant reports that lacked quantitative data are summarized qualitatively in Columns 32–39. Wherever our present, spotted microarray data and the Kudla AtGenExpress data showed similar patterns of expression for a given gene (i.e. up- or down-regulated by 2 or more fold in both data sets at a specific time point), this is indicated by the symbol 'Y' in the appropriate row of columns 32 or 33. Columns 34–39 contain the symbol 'Y' if the gene in that row was included in the lists of up-regulated genes reported in the following sources: Kreps et al. [12] (roots, 150 mM; 3 h, Column 34; 27 h, Column 35), Taji et al. [10] (roots, 250 mM, 2 h, Column 36), Maathuis et al. [13] (transporters only, unspecified tissues and NaCl concentration, Column 37), Kamei et al. [9] (Tables 1, 3, 5 of original report, genes up-regulated after 2 h or 5 h 250 mM treatment of sos2 or sos3 mutants, Column 38), Ma et al. [5] (Table 2 of original report, root-specific NaCl induced gene expression, Column 39).

Format: TXT Size: 2.3MB Download file

Additional File 2:

Assignment of genes to functional categories described in text. AGI identifiers and corresponding categories for the pathways or gene families named in Tables 2, 3, 4, 5, 6 of the manuscript. Authorities for assignment of AGIs to each category are cited in the respective legends of Tables 2, 3, 4, 5, 6. All genes in each category are listed here, regardless of their status in our microarray data. Some categories are further divided into sub-categories, which are denoted by double colons (::). This two column file may be used directly as input in STEM software [22].

Format: TXT Size: 190KB Download file