Table 2.

Number of reads sequenced and mapped with Tophat at each time point.

Time point	Block	Raw reads	Clean reads	Total mapped reads	Reads mapped to gene (%)
T4	A	55,101,326	52,359,821	39,568,121	99.00
	C	66,209,493	63,131,921	48,451,375	98.97
T5	A	53,179,667	51,277,891	39,809,444	98.90
	C	60,931,653	58,045,403	45,280,010	99.07
T6	A	52,067,162	50,169,858	38,980,092	98.97
	C	64,661,216	61,811,627	48,822,803	98.94
T8	C	56,984,949	54,509,265	42,577,251	98.74
	D	54,114,718	52,046,468	40,899,491	98.80
T9	C	51,186,386	48,646,447	38,516,348	98.83
	D	52,790,373	50,615,959	39,526,817	99.14

The average value of three biological replicates for each stage was calculated and used in the table.