Fig. S1 Laser microdissection of infected root tissues.

Fig. S2 MapMan representation of deregulated genes belonging to the ‘Mitochondrial electron transport’ functional category, using the mapping ‘Mt_AFFY_Mt3.0_0510.m02’.

Fig. S3 Number of probe sets deregulated in giant cells and surrounding cells classified into subcategories of the BIN class ‘Protein’ from the mapping ‘Mt_AFFY_Mt3.0_0510.m02’.

Table S1 Percentage of genes detected as expressed in Affymetrix gene chips

Table S2 Pearson correlation between biological replicates

Table S3 List of primers used for microarray validation by real-time PCR and promoter:GUS constructs

Table S4 List of statistically differentially expressed probe sets in at least one of our comparisons after Bonferroni correction (P < 0.05)

Table S5 List of nodule marker genes

Table S6 List of genes, possessing an orthologous gene in Arabidopsis, statistically differentially expressed in giant cells (GCs) and/or surrounding cells (SC) vs control cells from Medicago galls at 7-d post-infection relative to GC at 3 dpi from Arabidopsis (Barcala et al., 2010)

Table S7 Comparison between nodule zone II cells and whole-nodule transcriptomic data

Table S8 Nodule zone II cell-only deregulated processes

Table S9 List of deregulated probe sets coding for nodule-specific cysteine rich (NCR) or nodulins in nodule zone II cells, nodules at 10, 14 and 28 d post-infection

Table S10 Legume-specific genes deregulated in our analysis

Table S11 Differentially expressed transcription factor genes in our microarray experiments

Table S12 List of probe sets related to hormone metabolism and signalling deregulated in nodule zone II cells, giant cells and/or surrounding cells

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