TABLE 1.

Summary of RNA-Seq reads obtained and mapped to the UCSC mouse genome (mm10) by TopHat2 version 2.0.4^a

Sample	Sample group	Total reads	Total filtered reads	% filtered reads	Tophat2 total reads used	Tophat2 mapped reads	% Tophat2 mapped	% original reads mapped
ES594	WT	59,739,172	54,207,483	90.7%	51,675,521	48,601,337	94.1	81.4
ES595	WT	57,152,858	52,875,700	92.5	50,730,261	47,964,101	94.5	83.9
ES596	WT	58,833,186	54,250,597	92.2	51,983,177	48,554,589	93.4	82.5
ES597	WT	61,523,552	56,214,437	91.4	53,791,001	50,569,820	94.0	82.2
ES598	Double KO	57,775,842	53,563,505	92.7	51,429,249	48,165,044	93.7	83.4
ES600	Double KO	57,768,736	53,587,435	92.8	51,405,002	46,872,085	91.2	81.1
ES628	Double KO	58,727,920	54,463,663	92.7	52,325,308	49,201,172	94.0	83.8
ES629	Double KO	55,982,176	51,588,651	92.2	49,477,295	46,444,930	93.9	83.0
ES333	WT	122,435,492	117,028,201	95.6	113,414,331	105,959,643	93.4	86.5
ES334	WT	92,048,820	88,045,246	95.7	85,442,873	80,418,792	94.1	87.4
ES335	WT	111,930,898	106,605,448	95.2	103,046,163	97,020,593	94.2	86.7
ES336	WT	139,541,704	133,974,689	96.0	130,360,240	122,726,693	94.1	87.9
ES337	Triple KO	113,175,782	103,321,345	91.3	99,264,043	94,070,208	94.8	83.1
ES338	Triple KO	136,755,774	124,372,707	90.9	119,283,030	112,261,751	94.1	82.1
ES339	Triple KO	110,055,756	99,835,607	90.7	95,783,561	90,098,345	94.1	81.9
ES340	Triple KO	117,766,678	106,854,914	90.7	102,476,075	95,920,466	93.6	81.4

^aTotal reads as well as the percentage of reads removed for quality control are shown. In addition, the percentages of good-quality reads that were aligned to the reference genome are shown. Double KO group, four WT and four double KO spleen RNA samples sequenced on a lane of Illumina HiSeq2000 generated between 55 and 61 million raw reads per biological replicate. Triple KO group, four WT and four triple KO spleen RNA samples sequenced on a lane of Illumina HiSeq2000 generated between 92 and 139 million reads per biological replicate.