Table 1.

Stranded RNA-Seq Library Read and Mapping Summaries

Sample	Uniquely Mapped Reads: Replicate 1	Uniquely Mapped Reads: Replicate 2	Total Uniquely Mapped Reads	modENCODE/NCBI-SRA Accession Numbers
Third instar larvae, CNS	12,921,055	40,022,667	52,943,722	modENCODE_3466 SRR070409, SRR070410
Pupae, white pre-pupae + 2 days, CNS	44,833,331	37,635,655	82,468,986	modENCODE_3469 SRR100271, SRR070412
Mated female, eclosion + 4 days, heads	59,341,425	60,448,967	119,790,392	modENCODE_3448 SRR070414, SRR070415
Mated male, eclosion + 4 days, heads	54,635,860	54,555,328	109,191,188	modENCODE_3449 SRR070416, SRR070400
Mated female, eclosion + 4 days, ovaries	62,102,229	168,912,884	231,015,113	modENCODE_3451 SRR070431, SRR100277, SRR100283
Mated male, eclosion + 4 days, testes	249,972,580	171,471,971	421,444,551	modENCODE_3452 SRR070422, SRR350960, SRR070423, SRR100276, SRR350961
S2-R+	55,121,051	N/A	55,121,051	modENCODE_3487 SRR070279, SRR124149, SRR070266
Total	538,927,531	533,047,472	1,071,975,003

Details on RNA-seq data sets produced for this study. All the raw sequences reads and mapping files can be obtained under the designated accession numbers from the modENCODE Data Coordination Center (http://www.modencode.org/publications/dcc/index.shtml) and the NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/sra/).