Table 6.

Probe design summary for the AZ-specific microarray chip.

Transcript category	No. of transcripts	No. of probes per transcript	Total No. of probes
Annotated transcripts (RNA-Seq)	31,298	2 (1 sense and 1 antisense)	62,596
Novel transcripts (RNA-Seq)	8823	4 (2 sense and 2 antisense)	35,292
Annotated with Arabidopsis thaliana & Nicotiana tabacum	838	2 (1 sense and 1 antisense)	1676
Total No of transcripts resulted from RNA-Seq study	40,959
Previously reported transcripts related to the abscission process	356	2 (1 sense and 1 antisense)	712
Total No. of transcripts for Tomato Array	41,315		100,276
No. of probes collected after redundant/ probe selection criteria			93,674
Additional transcripts for technical quality control	50	4 (2 sense and 2 antisense)	200
No. of Agilent probes added in the Array		2 (1 sense and 1 antisense)	2278
Total No. of probes designed for Tomato Array	(93,674+200 + 2278) = 96,152
Total no of probes replicated to fill the remaining spots#	79,874
Total no of probes in the final array	176,026

The transcripts were obtained from various sources: RNA-Seq annotated and novel transcripts of the FAZ and LAZ prepared as detailed in Tables 1, 2; previously reported transcripts related to abscission (Meir et al., 2010; Wu et al., 2011), and additional transcripts obtained from Mark L. Tucker (USDA-ARS, USA). The probe was designed specifically for both sense and antisense orientations for the specific transcripts. The microarrays were designed for the transcripts listed in the table, using the Agilent custom gene expression microarray, 4X180K. The microarray was finalized with 176,026 probes including the technical quality and Agilent control grid probes.