Table 1.

Summary of the sample preparation and sequence profiles

Labela	Tissue/organ	Age/dev. stageb	Sex	Description	Platform (Hiseq)	Read length# (bp)	Total reads
HtN	Heart	Adult	Mixed	Ventricle, normal	2,000	101	55,882,914
HtR	Heart	Adult	Mixed	Ventricle, regenerating	2,000	101	50,516,110
Lb0	Limb	Adult	Mixed	Limb, normal	2,000	101	55,246,408
Lb3	Limb	Adult	Mixed	Limb, regenerating day3	2,000	101	47,286,228
Lb19	Limb	Adult	Mixed	Limb, regenerating day19	2,000	101	64,373,580
Tl	Tail	Adult	Female	Tail	2,500	125	27,630,846
Br	Brain	Adult	Female	Brain	2,500	125	27,626,778
Kn	Kidney	Adult	Female	Kidney	2,500	125	27,441,344
Lv	Liver	Adult	Female	Liver	2,500	125	30,427,600
Pc	Pancreas	Adult	Female	Pancreas	2,500	125	24,594,822
It	Intestine	Adult	Female	Intestine	2,500	125	28,214,656
Cn	Connective tissue	3 months juvenile	Male	Connective tissue adjacent to testis	2,000	106	34,403,376
Tg	Testicular gland	Adult	Male	Testicular gland, matured	2,000	106	33,182,908
Tt3	Testis	3 months juvenile	Male	Testis, not matured	2,000	106	36,052,648
TtA	Testis	Adult	Male	Testis, matured	2,000	106	35,305,096
Ov3	Ovary	3 months juvenile	Female	Ovary, not matured	2,000	106	37,990,436
Ov7	Ovary	7 months juvenile	Female	Ovary, not matured	2,000	106	39,617,046
Eg-1	Whole	Unfertilized egg	Unknown	Biological replicate 1	2,000	106	35,758,440
Eg-2	Whole	Unfertilized egg	Unknown	Biological replicate 2	2,000	106	38,172,320
St7	Whole embryo	Stage 7–7.5	Unknown	Early gastrula	2,500	125	29,361,580
St8b	Whole embryo	Stage 8b	Unknown	Slightly advanced early gastrula	1,500	100	65,423,479
St11	Whole embryo	Stage 11	Unknown	Middle-late gastrula	2,500	125	31,400,058
St12	Whole embryo	Stage 12	Unknown	Late gastrula	1,500	100	55,684,175
St15	Whole embryo	Stage 15	Unknown	Neural plate stage	1,500	100	48,604,306
St18	Whole embryo	Stage 18	Unknown	Late neural fold stage	1,500	100	55,446,723
St25-1	Whole embryo	Stage 25	Unknown	Elongated tail bud stage	1,500	100	49,345,987
St25-2	Whole embryo	Stage 25	Unknown	Tail bud stages (st25-28) were mixed.	2,000	101	51,692,566
St30-1	Whole embryo	Stage 30	Unknown	Gill protrusion stage	1,500	100	49,079,133
St30-2	Whole embryo	Stage 30	Unknown	st30 and st31were mixed.	2,000	101	49,920,498

^aAbbreviations correspond to the labels in Table 1, Figs 3, 5, and 7 and Supplementary Figs S2 and S3.

^bThe developmental stages were categorized according to criteria described by Shi and Boucaut.⁴³

#, paired end.