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Summary of protocols used in experiments 2 and 3. Cost is estimated per sample assuming a large number of libraries at US catalog prices as of May 2014, and includes RNA extraction.
Protocol Shorthand Cost/library
TruSeq TruS $45
Clontech CT $105
TotalScript TotS $115
Smart-seq2, standard protocol SS $55
Smart-seq2, 2.5 fold dilution SS—2.5x $28
Smart-seq2, 5 fold dilution SS—5x $20

\label{tab:protocolcosts}

Sequencing summary statistics for samples. Protocols are the shorthands used in table \ref{tab:protocolcosts}. Reads indicates the total number of reads, and Mapped the total number of reads that mapped at least once to either genome. Experiments 2 and 3 were run in a single HiSeq lane each.
Experiment Protocol % D. virilis Yield (fmole) Reads Mapped
2 CT 0 6.5 3,803,843 3,374,520
2 “ & 5 & 15.7 & 4,372,738 & 4,164,781
2 & ”		 10 47.4 10,013,087 9 ,527,023
2 “ & 20 & 17.8 & 4,781,463 & 4,317,101
2 & TotS & 0 & 176.8 & 3,281,134 & 2,930,058
2 & ”		 5 170.2 2,498,134 2,237,330
2 “ & 10 & 102.5 & 5,777,523 & 5,424,366
2 & ”		 20 119.9 6,068,996 5,740,496
2 TruS 0 2,401.0 67,560,511 64,024,881
2 “ & 5 & 2,001.1 & 23,370,854 & 22,589,083
2 & ”		 10 2,174.2 39,454,390 38,093,763
2 “ & 20 & 2,379.2 & 35,265,536 & 34,304,792
2 & SS2 & 0 & 34.3 & 2,439,518 & 2,297,087
2 & ”		 5 59.6 2,550,023 2,419,889
2 “ & 10 & 67.9 & 2,534,628 & 2,444,568
2 & ”		 20 39.8 2,504,340 2,389,850
3 SS2—2.5x 0 104.4 15,769,915 14,393,959
3 “ & 1 & 124.7 & 21,349,748 & 20,084,131
3 & ”		 5 113.0 17,047,120 16,329,641
3 “ & 10 & 103.5 & 23,762,232 & 22,372,562
3 & ”		 20 123.8 20,809,781 20,041,548
3 SS2—5x 0 59.4 19,214,155 17,324,598
3 “ & 1 & 58.6 & 23,832,274 & 22,364,220
3 & ”		 5 65.4 18,149,452 17,157,450
3 “ & 10 & 28.8 & 15,821,419 & 14,869,864
3 & ”		 20 57.2 22,466,345 21,620,603

\label{tab:protocols}