Table 1.

Summary of sequencing information: number of raw and clean reads, total and % of mapped reads onto minimal TAIR9 transcriptome, and reads with >1 RPKM, >500 RPKM, and >1000 RPKM of the five developmental stages: imbibed seed (yS), mature cotyledons (Cot), mature primary leaves (1L), mature secondary leaves (2L), and leaves of a 4-month-old plant (oL)

Mean >1 RPKM	yS			Cot			1L			2L			oL
	12252			13189			12832			12508			12849
	yS_1	yS_2	yS_3	Cot_1	Cot_2	Cot_3	1L_1	1L_2	1L_3	2L_1	2L_2	2L_3	oL_1	oL_2	oL_3
No. of raw reads (in m.)	30.55	33.71	31.25	30.43	38.26	34.46	37.41	37.83	25.54	30.46	37.89	36.38	29.87	35.74	35.47
No. of clean reads (in m.)	29.93	32.82	30.48	29.88	37.47	33.78	36.70	37.12	24.96	29.92	37.17	35.72	29.33	35.05	34.80
No. of clean reads (in %)	98.0	97.3	97.5	98.2	97.9	98.0	98.1	98.1	97.7	98.2	98.1	98.2	98.2	98.1	98.1
No. of mapped reads (in m.)	11.42	11.44	9.58	12.74	16.44	13.40	16.95	17.42	11.29	14.57	17.87	17.23	11.88	15.38	14.09
No. of mapped reads (in %)	37.4	33.9	30.7	41.9	43.0	38.9	45.3	46.0	44.2	47.8	47.2	47.4	39.8	43.0	39.7
No. of genes with >1 RPKM	11793	12498	11168	13161	13196	12974	12691	12902	12720	12423	12534	12535	12941	12608	12852
No. of genes with >500 RPKM	257	206	252	257	274	221	223	267	239	237	232	233	201	197	215
No. of genes with >1000 RPKM	109	82	118	81	90	86	84	94	80	86	86	88	83	84	83