Transcriptome data from tomato parthenocarpic mutants lacking SlDELLA

We investigated the behavior of tomato mutants lacking SlDELLA, a negative regulator of gibberellin (GA) signaling pathway. To focus on the early stages of anthesis, ovary samples of MicroTom-B (MT-B) and the mutant at the three stages (bud, flowering, and after flowering) were collected. We conducted three independent hybridizations with the GeneChip® Tomato Genome Array according to the manufacturer's instructions (Affymetrix, http:// www.affymetrix.com). A single biological replicate was utilized in each hybridization. The preprocessing and normalization/summarization of all CEL files were with the Bioconductor (Gentleman et al., 2004) and a robust multi-chip average (RMA) (Bolstad et al., 2003). The quality of GeneChip data was assessed by AFFYPLM package (Bolstad et al., 2005). We used the annotation of each gene in the CSV file Tomato.na32.annot.csv (downloaded on June 2011) released by the Affymetrix.