Extended Data Table 2. Summary of Total RNA-Seq Data from ldbr and U2AF RNAi experiments.

For each datasets the following information is included: Sample, Total reads, Mapped reads (from TopHat alignments), % mapped.

Sample	S2 Untreated	Idbr dsRNA	U2af38 dsRNA	U2af50 dsRNA	U2af38 & U2af50 dsRNA
Total reads	183,451,394	146,237,470	174,626,770	162,012,182	179,417,376
Mapped reads	66,597,777	54,762,604	56,120,630	43,620,982	61,437,507
% mapped	36.30%	37.45%	32.14%	26.92%	34.24%
# junctions	44,860	42,736	52,228	46,184	50,883
junctions/1 M reads	673.60	780.39	930.64	1058.76	828.21
# total junc reads	7,402,459	4,925,448	5,528,462	3,935,048	5,999,468
% junction reads	11.12%	8.99%	9.85%	9.02%	9.77%
# novel junction reads	2,369,949	1,575,057	1,337,830	919,616	1,273,867
% novel junctin reads	3.56%	2.88%	2.38%	2.11%	2.07%
# annotated junc reads	5,032,510	3,350,391	4,190,632	3,015,432	4,725,601
% annotated junction reads	7.56%	6.12%	7.47%	6.91%	7.69%
#novel junction cases	22,688	20,977	29,211	24,279	28,193
novel/total junctions	0.51	0.49	0.56	0.53	0.55
# annotated junc cases	22,172	21,759	23,017	21,905	22,690
annotated/total junctions	0.49	0.51	0.44	0.47	0.45
#RPs on both strands	119	100	81	64	0
RP/million reads	1.79	1.83	1.44	1.47	0.00
Total RP junc reads	1449	985	377	259	0
RP junc reads/million	21.76	17.99	6.72	5.94	0.00