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Figure S1. Functional categorization of the differentially expressed proteins identified from the rin mutant tomato fruit. The proteins were classified according to their biological roles and the FunCat annotation scheme (http://mips.gsf.de/proj/funcatDB). The 41 protein spots identified were categorized in 13 classes, i.e. amino acid metabolism, carbohydrate metabolism, lipid metabolism, secondary metabolism, glycolysis, Krebs cycle, photosynthesis/respiration, fermentation, protein modification, intracellular signaling, stress response, detoxification, and cytoskeleton.

Figure S2. Annotated spectra for proteins identified by a single peptide or multiple peptides with each ion scored below the threshold. Spot numbers were consistent with those in 2-DE gel.

Table S1. Identification of the differentially expressed proteins in the rin mutant tomato fruit using ESI-Q-TOF MS/MS

Table S2. Predicted RIN binding motifs within 2000-bp upstream region starting from ATG of each candidate target genes

Table S3. Primers used in the ChIP-qPCR analysis

Table S4. Scores and matched peptides of the identified proteins based on tandem mass spectrometry. Proteins were listed with an order consistent with those in Table S1. The numbers were consistent with those in 2-DE gel. Area highlighted in grey means that these protein spots were identified with only one matching peptide or by multiple peptides with each ion scored below the threshold. The annotated spectra for these proteins were present in Figure S2

Table S5. Primers for qRT-PCR analysis

Table S6. Sequences of the probes used in EMSA

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