Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis

BMC Genomics

Table 1 Microarray experimental design for time course and sex hierarchy experiments.

I. Time course experiment
Probe 1	Probe 2	Replicates	Time points (hr APF)
Wild type female (CS)	Reference	3	0, 24, 48, 72, 96
Wild type male (CS)	Reference	3	0, 24, 48, 72, 96
tud progeny female	Reference	3	0, 24, 48, 72, 96
tud progeny male	Reference	3	0, 24, 48, 72, 96
II. Sex determination hierarchy experiment*
Probe 1	Probe 2	Replicates	Time point (hr APF)	# of Genes ^†
Wild type female (CS)	Wild type male (CS)	4	48	7972
Wild type female (Berlin)	Wild type male (Berlin)	4	48
tud progeny female	tud progeny male	4	48	420
Wild type female (CS)	XX tra pseudomales	4	48	95
Wild type female (CS)	XX dsx ^Dpseudomales	4	48	173**
Wild type female (CS)	XX dsx intersexuals	4	48	154
Wild type male (CS)	XY dsx intersexuals	4	48	155

Probes, numbers of replicates, and the time points assayed are listed for each experiment. Chromosomal sex is indicated by XX or XY. * Sex determination hierarchy experiments were all performed with a dye-swap design (see Methods). ^† The number of genes in each experiment that is significantly differentially expressed. ** The DSX set was defined with an additional statistical test to eliminate potential false-negatives resulting from exclusion in the TRA set. Therefore, a gene's inclusion in the DSX set is not necessarily contingent on its presence in the TRA set. For a description of the definition of the DSX set, see Results and Discussion and Methods.

ISSN: 1471-2164