Order	SeqName	SeqType	IsAE	Lum_Epi	Lum_Epi2	Myo_Epi	Myo_Epi2	hESCs	StemLike	vHMECs
1	STAG3	Gene	0	3.55	1.61	5.18	2.88	7.41	2.15	2.20
2	339784	Transcript	0	0.00	0.00	1.26	0.00	0.00	0.00	0.00
3	317296	Transcript	0	0	0	0	0	0	0	0
4	379577	Transcript	0	0.00	0.00	0.64	0.00	2.25	0.00	0.00
5	394018	Transcript	0	0.13	0.00	0.34	0.00	0.00	0.00	0.00
6	ER1a	ExonRegion	0	0.43	0.00	0.01	1.04	0.07	0.00	0.00
7	E1a_E2a	KnownJunction	0	0.00	0.00	0.00	0.00	0.90	0.00	0.00
8	E2_Aa	NovelBoundary	0	5.17	5.88	6.64	12.81	9.15	0.00	15.85
9	ER2a	ExonRegion	0	0.52	1.51	4.12	7.29	7.54	3.27	4.35
10	E2_Da	NovelBoundary	0	6.78	10.25	8.71	6.50	4.47	5.49	17.38
11	E2a_E3a	KnownJunction	0	0.00	0.00	2.21	4.25	1.13	2.41	1.46
12	ER3a	ExonRegion	0	0.03	0.00	1.10	1.89	4.47	2.20	1.21
13	E3_Da	NovelBoundary	0	3.24	10.59	9.56	8.34	5.16	3.24	17.81
14	E3a_E4a	KnownJunction	0	0.00	0.00	1.65	0.00	1.96	2.65	0.85
15	E4_Aa	NovelBoundary	0	20.81	10.98	13.11	16.36	0.00	29.16	23.78
16	ER4a	ExonRegion	0	7.66	7.76	13.29	11.93	34.13	7.56	16.91
17	E4_Da	NovelBoundary	0	15.47	6.41	18.70	12.38	40.83	2.12	26.93
18	E4a_E5a	KnownJunction	0	0.85	0.00	0.00	0.00	8.64	1.66	0.82
19	E4a_E34a	NovelJunction	0	7.41	1.05	6.15	19.40	2.19	0.00	1.58
20	E4a_E35a	NovelJunction	0	2.67	4.47	6.44	10.19	0.00	0.00	0.00
21	ER5a	ExonRegion	0	1.17	1.42	2.72	5.06	6.50	2.22	1.02
22	E5a_E6a	KnownJunction	0	8.81	1.52	9.56	8.32	3.30	5.44	3.54
23	ER6a	ExonRegion	0	13.63	6.44	8.27	3.09	9.60	8.61	1.84
24	E6_Da	NovelBoundary	0	43.83	7.72	27.53	13.14	17.70	4.42	12.63
25	E6a_E7a	KnownJunction	0	2.72	3.26	0.00	1.68	2.19	1.58	1.28
26	E6a_E7b	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
27	ER7a	ExonRegion	0	0.16	0.01	0.73	0.86	3.23	2.98	0.79
28	E7_Ab	KnownBoundary	0	15.42	21.02	17.65	11.08	36.65	18.52	33.06
29	ER7b	ExonRegion	0	1.10	0.00	1.23	0.00	5.21	0.00	1.83
30	E7a_E8a	KnownJunction	0	0.00	0.00	0.72	0.00	6.55	0.00	1.53
31	ER8a	ExonRegion	0	1.07	0.00	2.89	0.64	5.33	1.23	1.70
32	E8a_E9a	KnownJunction	0	0.00	0.00	0.88	0.00	4.45	0.00	1.98
33	I8_SR3	SilentIntronRegion	0	1.85	0.81	9.65	2.19	3.41	3.20	0.52
34	E9_Aa	NovelBoundary	0	2.90	0.00	10.15	4.31	1.04	2.87	0.73
35	ER9a	ExonRegion	0	1.26	0.00	3.23	4.01	5.08	0.00	3.66
36	E9_Da	NovelBoundary	0	7.81	1.02	25.35	4.50	11.69	7.32	0.89
37	E9a_E10a	KnownJunction	0	0.00	0.00	1.49	5.23	5.46	0.00	4.14
38	I9_AR1	ActiveIntronRegion	0	4.99	0.40	12.56	3.48	3.47	4.83	0.66
39	ER10a	ExonRegion	0	0.01	0.00	0.64	3.06	4.25	0.00	1.63
40	E10a_E11a	KnownJunction	0	0.00	0.00	0.00	4.04	3.46	0.00	2.58
41	I10	Intron	0	2.68	1.30	11.21	4.18	2.47	6.88	0.41
42	I10_SR1	SilentIntronRegion	0	2.69	1.31	11.26	4.20	2.49	6.91	0.41
43	E11_Aa	NovelBoundary	0	1.60	1.00	13.12	4.14	2.21	5.39	1.43
44	ER11a	ExonRegion	0	1.75	0.00	2.65	5.57	6.11	0.94	0.96
45	E11a_E12a	KnownJunction	0	0.00	0.00	0.76	0.00	5.30	0.00	0.00
46	E12_Aa	NovelBoundary	0	0.95	0.00	10.53	4.80	4.38	12.65	0.00
47	ER12a	ExonRegion	0	0.00	0.00	2.09	0.62	3.91	0.00	0.03
48	E12_Da	NovelBoundary	0	0.90	0.00	12.01	8.15	1.06	3.94	2.55
49	E12a_E13a	KnownJunction	0	0.00	0.00	1.51	1.68	4.93	0.00	0.00
50	E13_Aa	NovelBoundary	0	0.58	0.00	9.51	5.12	1.04	3.78	0.89
51	ER13a	ExonRegion	0	1.04	0.00	3.66	1.66	4.30	1.73	0.59
52	E13_Da	NovelBoundary	0	0.00	0.00	9.87	8.75	5.39	1.37	0.82
53	E13a_E14a	KnownJunction	0	0.00	0.00	0.89	2.55	5.07	0.00	0.75
54	ER14a	ExonRegion	0	0.00	0.00	2.02	2.91	4.94	4.04	1.23
55	E14a_E15a	KnownJunction	0	0.00	0.00	1.97	0.00	4.47	0.00	0.00
56	E15_Aa	NovelBoundary	0	1.03	3.26	2.66	5.31	4.24	12.11	0.70
57	ER15a	ExonRegion	0	0.00	0.00	1.97	0.89	4.03	1.19	0.92
58	E15a_E16a	KnownJunction	0	0.00	0.00	0.00	0.00	2.90	2.81	0.00
59	E16_Aa	NovelBoundary	0	51.29	10.75	47.31	12.27	54.59	11.68	81.52
60	ER16a	ExonRegion	0	0.37	0.02	1.95	0.94	3.38	1.47	0.06
61	E16a_E17a	KnownJunction	0	0.00	0.00	1.52	0.00	2.84	0.00	0.00
62	ER17a	ExonRegion	0	0.00	1.96	4.92	3.49	7.04	1.00	0.69
63	E17a_E18a	KnownJunction	0	0.00	0.00	1.64	1.68	3.27	0.00	0.87
64	E18_Aa	NovelBoundary	0	1.59	2.65	11.02	5.31	5.46	0.00	0.00
65	ER18a	ExonRegion	0	0.00	1.00	4.18	2.58	3.89	1.38	0.34
66	E18_Da	NovelBoundary	0	1.82	1.08	8.90	2.95	0.92	0.00	1.20
67	E18a_E19a	KnownJunction	0	0.00	0.00	3.13	0.00	5.56	1.58	0.00
68	ER19a	ExonRegion	0	0.29	0.00	3.43	0.83	5.04	1.05	0.15
69	E19_Da	NovelBoundary	0	1.03	4.05	7.54	8.51	3.04	6.32	1.65
70	E19a_E20a	KnownJunction	0	0.00	0.00	1.64	1.44	3.32	1.58	0.87
71	E20_Aa	NovelBoundary	0	15.77	6.44	48.20	7.96	10.81	19.99	12.87
72	ER20a	ExonRegion	0	0.37	0.26	1.13	1.60	3.58	3.68	0.29
73	E20_Da	NovelBoundary	0	4.16	8.43	29.39	8.56	7.68	8.01	4.01
74	E20a_E21a	KnownJunction	0	1.03	1.21	2.13	1.03	6.11	3.64	0.00
75	E21_Aa	NovelBoundary	0	12.00	15.71	44.33	8.02	25.04	12.46	13.36
76	ER21a	ExonRegion	0	0.36	1.71	1.60	0.10	5.87	2.70	0.03
77	E21_Da	NovelBoundary	0	1.80	5.60	28.70	0.00	10.17	7.21	5.17
78	E21a_E22a	KnownJunction	0	0.00	1.16	3.82	0.00	9.91	7.34	0.72
79	E22_Aa	NovelBoundary	0	21.36	6.96	75.34	16.36	29.07	8.42	5.65
80	ER22a	ExonRegion	0	0.15	0.28	3.13	0.31	4.15	4.93	0.67
81	E22_Da	NovelBoundary	0	10.11	4.02	41.69	1.68	25.84	4.21	5.60
82	E22a_E29b	KnownJunction	0	0.00	0.00	2.51	0.00	0.00	0.00	0.00
83	E22_Db	NovelBoundary	0	9.80	8.14	37.62	18.26	25.91	0.00	3.96
84	E22b_E23a	KnownJunction	0	1.85	0.00	0.89	3.33	3.34	0.00	0.00
85	ER22b	ExonRegion	0	0.77	0.00	1.44	2.49	2.87	0.00	0.42
86	E23_Aa	NovelBoundary	0	6.73	11.77	49.22	14.68	19.39	13.32	3.27
87	ER23a	ExonRegion	0	0.34	0.00	2.29	1.21	3.98	3.01	0.00
88	E23_Da	NovelBoundary	0	4.81	6.12	38.94	14.06	11.71	15.62	4.86
89	E23a_E24a	KnownJunction	0	0.00	0.00	4.07	0.00	10.90	0.00	0.00
90	E24_Aa	NovelBoundary	0	7.46	6.52	36.76	7.15	15.79	15.89	3.17
91	ER24a	ExonRegion	0	0.58	0.00	1.79	1.10	4.31	2.20	0.20
92	E24_Da	NovelBoundary	0	2.75	4.97	23.25	10.51	4.82	11.93	3.64
93	E24a_E25a	KnownJunction	0	0.00	0.00	1.31	0.00	3.09	4.50	0.82
94	E25_Aa	NovelBoundary	0	4.99	10.48	30.47	4.28	8.99	15.62	4.80
95	ER25a	ExonRegion	0	0.01	0.00	2.21	0.00	3.12	1.63	0.84
96	E25_Da	NovelBoundary	0	1.67	1.18	14.21	1.27	5.79	3.27	1.52
97	E25a_E26a	KnownJunction	0	0.00	0.00	2.92	0.00	5.81	1.61	2.32
98	ER26a	ExonRegion	0	1.67	0.00	4.42	0.00	9.61	0.83	2.21
99	E26a_E27a	KnownJunction	0	0.00	0.00	1.87	0.00	14.92	1.42	0.87
100	ER27a	ExonRegion	0	1.37	0.62	5.41	1.27	8.66	1.07	1.41
101	E27a_E28a	KnownJunction	0	0.75	0.00	0.00	0.00	7.54	0.00	1.86
102	ER28a	ExonRegion	0	3.04	1.43	6.08	2.23	11.58	3.60	2.42
103	E28a_E29a	KnownJunction	0	3.15	1.23	0.86	2.25	7.35	0.00	0.89
104	ER29a	ExonRegion	0	2.75	1.11	2.41	1.10	9.74	2.87	2.50
105	E29_Ab	KnownBoundary	0	0.92	2.31	4.74	0.00	3.48	3.48	2.57
106	ER29b	ExonRegion	0	1.73	1.39	4.52	0.76	2.85	0.56	0.80
107	E29a_E30a	KnownJunction	0	0.00	1.08	0.00	1.60	2.97	0.00	0.64
108	E30_Aa	NovelBoundary	0	3.59	3.63	12.01	3.28	17.87	3.11	2.85
109	ER30a	ExonRegion	0	0.66	0.46	1.16	0.21	4.24	0.53	0.64
110	E30_Da	NovelBoundary	0	15.77	1.58	36.10	1.35	29.60	4.66	6.15
111	E30a_E31a	KnownJunction	0	0.00	0.00	0.66	0.00	0.00	0.00	0.00
112	E30a_E31b	KnownJunction	0	0.00	0.00	0.00	0.00	2.24	0.00	0.00
113	E31_Aa	NovelBoundary	0	0.67	0.00	14.59	4.50	15.47	0.00	0.00
114	E31_Ab	NovelBoundary	0	9.71	0.00	13.84	4.14	8.37	1.66	0.56
115	ER31a	ExonRegion	0	0.00	0.00	0.68	0.00	2.02	0.00	0.00
116	ER31b	ExonRegion	0	0.00	0.00	1.35	0.00	4.21	0.00	1.02
117	E31_Da	NovelBoundary	0	6.61	6.52	32.51	6.10	14.87	1.66	11.48
118	E31a_E32a	KnownJunction	0	0.00	0.00	0.60	0.00	6.69	0.00	0.00
119	E32_Aa	NovelBoundary	0	5.26	7.67	28.11	2.09	17.47	0.00	8.15
120	ER32a	ExonRegion	0	0.00	0.01	2.45	0.20	3.13	1.09	1.01
121	E32_Da	NovelBoundary	0	5.74	2.78	31.08	0.00	20.98	2.65	4.20
122	E32a_E33a	KnownJunction	0	0.72	0.00	2.85	1.19	5.60	0.00	2.67
123	Ix	Intron	0	7.50	0.89	18.58	0.69	15.37	0.45	1.10
124	Ix_AR1	ActiveIntronRegion	0	8.53	0.99	22.62	1.06	17.75	0.54	1.39
125	Ix_SR1	SilentIntronRegion	0	9.54	1.39	21.50	0.11	11.26	0.57	1.15
126	Ix_SR2	SilentIntronRegion	0	1.61	0.00	0.96	0.00	11.70	0.00	0.00
127	Ix	Intron	0	2.84	2.17	12.17	0.22	9.78	0.44	2.29
128	Ix_AR1	ActiveIntronRegion	0	2.84	2.17	12.20	0.22	9.80	0.44	2.29
129	E33_Aa	NovelBoundary	0	3.69	1.31	8.49	0.00	8.39	0.00	4.04
130	ER33a	ExonRegion	0	0.57	1.20	5.31	1.97	6.96	0.05	0.98
131	E33_Da	NovelBoundary	0	4.32	1.05	6.12	0.00	10.44	1.18	2.54
132	E33a_E34a	KnownJunction	0	0.00	0.00	1.29	1.52	5.76	0.00	0.00
133	E33a_E35a	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
134	E34_Aa	NovelBoundary	0	23.77	12.35	29.99	8.37	14.96	4.88	8.00
135	ER34a	ExonRegion	0	28.10	10.36	26.40	11.43	19.61	4.63	8.28
136	E34_Da	NovelBoundary	0	32.36	8.41	19.89	10.97	17.36	4.50	5.52
137	Ix	Intron	0	5.09	1.69	10.90	1.37	10.18	0.45	2.42
138	Ix_SR1	SilentIntronRegion	0	5.12	2.02	10.81	0.00	7.83	0.00	2.50
139	Ix_AR2	ActiveIntronRegion	0	5.49	2.56	9.15	1.94	7.68	0.12	2.76
140	Ix_SR2	SilentIntronRegion	0	6.10	0.70	15.46	2.37	10.59	1.05	2.67
141	Ix_AR4	ActiveIntronRegion	0	5.66	1.60	14.23	0.62	16.24	0.81	2.67
142	Ix_SR4	SilentIntronRegion	0	1.66	0.00	8.37	0.00	9.79	0.57	1.25
143	E35_Aa	NovelBoundary	0	194.24	39.67	237.80	113.59	47.24	31.14	16.38
144	ER35a	ExonRegion	0	0.00	0.00	1.21	0.00	6.96	0.00	0.00
145	E35_Da	NovelBoundary	0	41.24	19.73	46.20	17.96	28.68	3.03	19.13
146	Ix	Intron	0	8.60	3.11	23.41	0.84	24.49	0.66	2.73
147	Ix_SR1	SilentIntronRegion	0	9.16	3.29	24.93	0.84	25.91	0.73	2.96
148	Ix_AR1	ActiveIntronRegion	0	2.77	1.32	7.36	0.92	9.65	0.00	0.28
149	Ix	Intron	0	21.53	12.23	45.30	9.26	30.19	0.59	11.38
150	Ix_AR1	ActiveIntronRegion	0	21.66	12.30	45.58	9.32	30.35	0.59	11.44
151	Ix	Intron	0	4.66	3.69	11.85	2.47	12.92	0.29	2.12
152	Ix_SR1	SilentIntronRegion	0	5.39	4.16	13.67	2.89	14.64	0.34	2.49
153	ER36a	ExonRegion	0	0.13	0.00	0.34	0.00	0.00	0.00	0.00