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Figure S1. Experimental design of the four microarray studies.

Figure S2. Cluster analysis of photosynthesis-related genes DE in developing buds under SD.

Figure S3. Cluster analysis of cell wall-related genes DE in developing buds under SD.

Figure S4. Cluster analysis of DE TFs in developing buds under SD.

Figure S5. Cluster analysis of DE regulators implicated in developmental processes occurring in developing buds under SD.

Figure S6. Comparison of the expression pattern of selected genes by qPCR and on the microarrays.

Figure S7. Cluster analysis of hormone associated genes DE in developing buds under SD.

Table S1. Genes and gene-specific primers used for qRT-PCR.

Table S2. K-means clustering of DE genes in developing buds under SD.

Table S3. Regulatory genes, including transcription factors, DE in developing buds under SD.

Table S4. DE genes in developing buds under LD.

Table S5. Genes DE in developing buds under both LD and SD.

Table S6. Genes uniquely DE in developing buds under SD.

Table S7. Genes expressed at significantly higher levels in developing buds relative to stems and needles under SD.

Table S8. Genes both uniquely DE and expressed at significantly higher levels in developing buds relative to stems and needles under SD.

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