Supporting Information Legends
Figure S1. Comparison of transcriptomes of 3 bioreplicates each of WT, rsh mutant
and ANP4-F2
The heat map of the nine samples was generated using pair-wise Pearson correlation
coefficients of gene expression values. MultiExperiment Viewer (MeV) was used for
sample clustering. Note the closer correlation of the ANP4 to WT, while the
mutant shows less correlation to either. Also note the degree of consistency between
bioreplicates. The highest correlation is red; lowest correlation is green.
Figure S2. Phenotypes of seedlings used in this study and summary data from
differential gene expression tested by microarray analysis
(a) Seedlings of WT, ANP4-F2, ANP4-F3, ANP10-F3 and rsh mutant at 12 DAS on
vertically incubated plates. (b) Numbers of genes with ≥2 fold differential gene expression
(P ≤ 0.05) in comparisons of rsh mutant to WT, ANP4-F2 to mutant, and ANP4-F2 to WT.
Of the 21,560 genes analyzed the figure shows a breakdown of genes down- (dn) and upregulated. *, of the 1,772 genes down-regulated in the rsh mutant vs WT, 1,311 of them
plus 538 other genes were up-regulated in the ANP4-F2; †, out of the 1,218 genes upregulated in the rsh mutant vs WT, 949 of them plus 277 other genes were down-regulated
in the ANP4-F2 vs the rsh mutant.
Figure S3. Comparative expression of genes from selected families with ≥2 fold
differential expression (P ≤ 0.05) in at least one of the three comparisons made
between three samples i.e., WT, rsh mutant and ANP4-F2, using microarray analysis
of seedlings
(a) 33 (putative) AGP genes. (b) 40 (putative) PER genes. (c) 17 (putative) EXP/EXPL
genes. (d) 3 (putative) P4H genes. Genes were clustered based on Pearson correlation
coefficients of mean transcript levels (normalized signal intensity). Bargraphs represent
percentages of the total combined mean transcript levels for one gene in the three samples
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being compared i.e., one bargraph row compares expression of an individual gene between
the three samples. Superscripts1, 2 indicate significance (P ≤ 0.05) of rsh mutant vs WT and
ANP4-F2 vs WT, respectively (also see Table S6). The heatmaps are Log2 of these same
mean expression values for each gene used in the bargraphs. The color scale shows the
highest (red) to lowest (white) transcript signals obtained. Each heatmap column (vertical)
shows expression of each gene within one sample, while each heatmap row allows a broad
color image comparison of the expression of each individual gene between the three
samples. For EXT and PRP data see Table S6. For gene names and accessions, see Tables
S5 and S6.
Table S1. Top 50 (putative) genes down-regulated in the rsh mutant vs WT, and their
expression in the ANP4-F2 vs the rsh mutant, by microarray analysis of seedlings
Table S2. Top 50 (putative) genes up-regulated in the rsh mutant vs WT, and their
expression in the ANP4-F2 vs the rsh mutant, by microarray analysis of seedlings
Table S3. Top 50 (putative) genes down-regulated in the ANP4-F2 vs WT, by microarray
analysis of seedlings
Table S4. Top 50 (putative) genes up-regulated in ANP4-F2 vs WT, by microarray analysis
of seedlings
Table S5. Abbreviations, full names/descriptions of (putative) gene products
Table S6. EXT, PRP, AGP, PER, EXP/EXPL and P4H (putative) genes showing ≥2 fold
differential expression in at least one of the following three comparisons (and reverse
comparisons) of WT, the rsh mutant, and ANP4-F2 seedlings, by microarray analysis (also
see Figure S3)
2
Table S7. Expression comparisons of all 65 EXT and 18 PRP, and selected 10 AGP, 15
PER, 8 EXP/EXPL, 3 P4H, and 14 DBP and 3 kinase encoding (putative) genes in WT, rsh
mutant and ANP4-F2, by qRT-PCR analysis of seedlings (also see Figure 2)
Table S8. Expression comparisons of ANP4-F3 and ANP10-F3 with WT-2 (next
generation WT), for all 65 EXT and 18 PRP, and for selected 10 AGP, 15 PER,
8 EXP/EXPL, 3 P4H, and 14 DBP and 3 kinase encoding (putative) genes, by qRT-PCR
analysis of seedlings (also see Figure 4)
Table S9. Amino acid composition as average mole % of total amino acids in cell walls of
seedling roots from WT, rsh mutant, ANP4-F2 and ANP10-F2
Table S10. Primers used for qRT-PCR, and PCR (last two lines)
Experimental procedures for supporting information
References for supporting information
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