Transcriptome data from tomato parthenocarpic mutants lacking Aux/IAA transcription factor SlIAA9

We investigated the behavior of tomato mutants lacking transcription factors of SlIAA9, a key gene controlling parthenocarpy. To focus on the early stages of anthesis, ovary samples of MicroTom-J (MT-J) 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. This dataset includes 2 experimental batches. Therefore, a batch adjustment for unwanted variation [e.g., ComBat (Johnson et al., 2007)] is needed for further downstream analyses.