Order	SeqName	SeqType	IsAE	Lum_Epi	Lum_Epi2	Myo_Epi	Myo_Epi2	hESCs	StemLike	vHMECs
1	TLE4	Gene	0	91.40	147.67	76.87	277.41	91.27	264.56	43.10
2	376552	Transcript	0	1.25	1.45	0.89	2.41	0.38	2.99	0.16
3	399288	Transcript	0	26.08	69.60	12.23	115.29	11.07	69.09	25.47
4	265284	Transcript	0	0	0	0	0	0	0	0
5	376540	Transcript	0	0.60	0.32	0.19	1.29	0.16	0.08	0.08
6	376527	Transcript	0	4.09	4.76	1.97	1.68	4.61	5.17	0.00
7	376544	Transcript	1	15.29	23.09	18.12	148.32	1.04	165.01	2.29
8	376525	Transcript	0	3.65	2.47	7.19	8.58	0.00	0.00	0.55
9	376537	Transcript	0	0	0	0	0	0	0	0
10	376534	Transcript	1	1.03	0.00	0.89	16.53	0.00	18.01	0.00
11	376524	Transcript	1	22.18	4.23	12.55	7.52	0.27	4.02	0.00
12	376522	Transcript	0	7.89	6.65	7.44	6.45	0.53	3.36	1.24
13	376520	Transcript	0	0	0	0	0	0	0	0
14	ER1a	ExonRegion	0	2.50	2.90	1.77	4.82	0.75	5.98	0.31
15	E1_Ab	KnownBoundary	1	33.91	25.38	18.52	40.07	0.92	48.40	2.01
16	ER1b	ExonRegion	1	53.98	83.10	60.63	158.00	17.10	167.28	9.95
17	E1_Ac	KnownBoundary	0	8.68	14.71	5.96	43.75	3.30	45.75	3.67
18	ER1c	ExonRegion	1	25.96	48.00	13.07	98.38	16.16	82.12	3.99
19	E1_Ad	KnownBoundary	1	48.05	84.94	29.59	162.30	29.39	129.15	7.09
20	ER1d	ExonRegion	0	43.70	128.74	40.29	246.88	40.82	191.93	17.72
21	E1a_E3a	KnownJunction	0	60.68	140.74	64.72	310.17	74.99	192.69	25.18
22	ER2a	ExonRegion	0	0.38	2.70	0.00	0.59	0.00	1.33	0.00
23	E2_Ab	KnownBoundary	0	0.73	5.25	1.52	3.90	1.04	2.95	0.59
24	ER2b	ExonRegion	0	1.27	6.30	0.50	6.63	0.21	8.36	1.56
25	E2a_E3a	KnownJunction	0	2.60	6.52	0.56	11.27	0.00	12.68	3.70
26	ER3a	ExonRegion	0	157.18	262.82	139.11	501.25	132.59	351.87	46.51
27	E3a_E4a	KnownJunction	0	212.25	314.68	163.98	642.19	159.27	469.32	70.32
28	E3a_E9b	NovelJunction	1	0.00	4.68	0.00	1.22	0.00	11.01	0.00
29	E4_Aa	NovelBoundary	1	87.91	3.73	72.74	12.49	0.00	11.60	0.00
30	ER4a	ExonRegion	0	191.76	340.01	175.94	651.34	166.41	430.59	76.25
31	E4_Da	KnownBoundary	0	5.41	1.63	13.47	12.60	0.00	0.00	0.00
32	E4a_E5a	KnownJunction	0	132.85	298.84	150.76	553.55	178.68	361.98	70.57
33	E4a_E6a	KnownJunction	1	1.03	0.00	0.89	16.53	0.00	18.01	0.00
34	E4a_E9a	NovelJunction	1	0.80	0.00	0.00	19.02	0.00	19.64	0.00
35	ER4b	ExonRegion	0	3.65	2.47	7.19	8.58	0.00	0.00	0.55
36	ER5a	ExonRegion	0	194.60	295.24	186.24	494.43	157.06	353.74	79.42
37	E5_Da	KnownBoundary	1	43.28	10.17	23.85	16.39	1.89	8.23	0.00
38	E5a_E6a	KnownJunction	0	157.05	212.38	137.41	366.35	129.40	273.22	70.02
39	E5a_E7a	NovelJunction	0	10.77	16.60	7.10	47.49	6.50	35.51	2.92
40	E5a_E8a	NovelJunction	0	0.95	1.63	0.73	3.22	1.18	9.97	0.00
41	E5a_E9a	NovelJunction	0	4.01	12.08	2.90	43.94	2.26	36.53	0.77
42	E5a_E13a	NovelJunction	1	3.50	0.00	1.57	4.14	0.00	10.18	0.00
43	ER5b	ExonRegion	1	22.18	4.23	12.55	7.52	0.27	4.02	0.00
44	E5_Db	NovelBoundary	1	23.25	9.96	26.04	5.47	0.00	15.03	0.00
45	I5_AR2	ActiveIntronRegion	1	19.32	2.33	14.51	12.95	0.98	2.36	0.91
46	I5_AR3	ActiveIntronRegion	1	45.12	10.12	30.50	49.31	4.55	30.16	2.39
47	I5_SR4	SilentIntronRegion	1	34.12	10.25	31.35	36.37	3.30	24.34	1.68
48	I5_AR4	ActiveIntronRegion	1	19.00	7.27	19.63	18.91	2.29	13.41	1.16
49	I5_SR5	SilentIntronRegion	1	12.50	1.57	16.82	17.85	5.45	11.06	1.18
50	I5_AR5	ActiveIntronRegion	1	17.05	1.66	16.16	17.62	0.91	12.85	1.06
51	I5_AR6	ActiveIntronRegion	1	21.77	1.82	24.30	15.84	0.40	10.63	0.67
52	I5_AR7	ActiveIntronRegion	1	24.77	2.64	26.67	12.08	1.48	11.60	0.44
53	I5_AR9	ActiveIntronRegion	1	21.97	5.83	15.92	15.38	1.74	9.56	0.83
54	E6_Aa	NovelBoundary	1	64.94	3.97	69.51	12.60	0.00	4.58	0.60
55	ER6a	ExonRegion	0	143.58	247.64	139.51	397.50	129.43	259.62	84.46
56	E6a_E7a	KnownJunction	0	110.95	233.32	97.69	326.53	89.84	205.39	73.86
57	E6a_E8a	NovelJunction	0	2.97	5.18	2.24	8.37	0.90	10.05	1.36
58	E6a_E9a	NovelJunction	1	14.44	25.25	20.31	68.87	26.79	51.83	0.62
59	E6a_E9b	NovelJunction	1	10.20	13.00	8.84	52.04	12.75	29.56	0.00
60	ER7a	ExonRegion	0	109.47	237.53	95.83	305.81	96.02	228.08	76.14
61	E7_Da	KnownBoundary	0	10.71	5.20	8.29	12.87	0.00	5.84	3.04
62	E7a_E8a	KnownJunction	1	17.52	66.05	6.25	103.41	2.21	49.53	36.76
63	E7a_E9a	NovelJunction	0	30.51	49.52	24.19	55.97	28.24	49.90	20.98
64	E7a_E9b	KnownJunction	0	52.21	131.70	59.08	135.73	65.47	152.76	33.95
65	E7a_E13a	NovelJunction	0	5.84	2.55	1.68	8.67	0.00	10.56	1.40
66	ER7b	ExonRegion	0	15.39	10.61	14.87	12.31	1.06	5.40	2.48
67	ER8a	ExonRegion	1	30.15	81.80	9.67	136.46	5.30	80.10	32.16
68	E8a_E9a	KnownJunction	0	25.30	70.75	10.02	116.82	5.12	65.02	16.12
69	E8a_E9b	NovelJunction	0	6.19	7.25	1.61	24.35	0.00	26.67	5.23
70	E9_Ab	NovelBoundary	1	26.57	3.05	17.42	7.50	0.00	1.23	0.00
71	ER9a	ExonRegion	0	57.44	126.95	34.55	218.53	41.91	149.57	42.33
72	ER9b	ExonRegion	0	113.03	248.96	105.63	411.80	122.91	379.42	76.23
73	E9a_E11a	KnownJunction	0	94.53	202.37	84.81	380.01	178.13	372.14	68.56
74	E9a_E12a	KnownJunction	0	0.00	0.00	0.53	0.00	0.00	0.00	0.00
75	E9a_E13a	NovelJunction	1	7.68	16.37	4.37	19.10	0.00	40.41	1.46
76	E9a_E13c	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
77	E9b_E10a	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
78	ER9c	ExonRegion	0	0.00	2.43	1.35	1.25	0.81	1.23	0.00
79	ER9d	ExonRegion	0	0.00	2.43	0.68	1.25	0.81	1.23	0.00
80	E10a_E13b	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
81	ER10a	ExonRegion	0	0.77	1.30	0.77	2.24	0.65	0.33	0.31
82	I10	Intron	1	16.72	4.96	17.61	9.93	3.02	3.86	1.26
83	I10_SR2	SilentIntronRegion	1	17.58	5.10	18.71	10.83	3.29	4.25	1.26
84	E11a_E13a	KnownJunction	0	100.24	204.42	90.48	314.74	144.33	277.81	56.08
85	ER11a	ExonRegion	0	149.57	314.36	138.11	527.91	217.56	491.34	100.75
86	I11_AR1	ActiveIntronRegion	1	24.36	5.53	12.45	12.10	2.59	4.94	1.47
87	I11_AR4	ActiveIntronRegion	0	20.24	10.39	12.36	30.56	1.84	22.69	1.72
88	E12a_E13c	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
89	ER12a	ExonRegion	0	0.11	0.22	0.25	0.32	0.09	0.14	0.00
90	I12_SR3	SilentIntronRegion	1	19.86	9.65	9.07	8.39	0.83	4.92	0.78
91	I12_AR3	ActiveIntronRegion	1	26.22	16.24	12.97	18.29	1.92	14.45	1.62
92	I12_SR4	SilentIntronRegion	1	25.50	13.66	13.33	13.64	4.09	12.92	1.13
93	I12_AR4	ActiveIntronRegion	1	24.76	15.66	14.65	11.74	2.16	22.32	0.37
94	E13_Ac	NovelBoundary	0	112.41	197.64	95.28	321.76	71.39	281.53	52.40
95	ER13a	ExonRegion	0	157.53	319.91	155.57	538.69	201.38	481.41	97.14
96	ER13b	ExonRegion	0	167.62	331.66	159.61	536.97	193.86	472.78	99.00
97	ER13c	ExonRegion	0	204.97	378.13	184.76	665.24	169.69	636.12	107.40
98	E13a_E14a	KnownJunction	0	165.48	349.09	161.45	515.11	259.87	509.06	120.28
99	E13a_E17a	KnownJunction	1	15.29	23.09	18.12	148.32	1.04	165.01	2.29
100	ER14a	ExonRegion	0	205.40	311.05	182.74	491.58	196.01	536.24	129.76
101	E14a_E15a	KnownJunction	0	169.62	229.56	141.66	383.12	148.76	465.16	102.33
102	E14a_E16a	KnownJunction	0	1.62	0.00	0.00	2.90	0.00	0.00	0.00
103	E14a_E17a	NovelJunction	0	42.69	52.57	36.80	86.99	19.23	63.30	12.12
104	ER15a	ExonRegion	0	149.14	242.57	128.13	420.51	129.72	422.79	98.63
105	E15a_E16a	KnownJunction	0	4.09	4.76	1.97	1.68	4.61	5.17	0.00
106	E15a_E17a	KnownJunction	0	174.53	222.78	149.71	449.79	223.57	407.30	119.17
107	I15_AR1	ActiveIntronRegion	1	27.33	2.43	23.42	20.13	0.81	11.03	0.00
108	I15_SR2	SilentIntronRegion	1	24.63	3.56	21.79	18.05	1.35	5.55	0.05
109	E16_Aa	NovelBoundary	1	17.14	10.75	20.28	19.67	0.00	5.76	0.83
110	ER16a	ExonRegion	0	16.08	4.82	6.79	12.81	7.77	13.15	1.15
111	E16_Da	NovelBoundary	1	26.05	12.48	27.98	10.35	1.04	5.84	1.42
112	E16a_E17a	KnownJunction	0	8.29	3.10	3.12	5.99	5.46	2.79	0.00
113	E17_Aa	NovelBoundary	1	45.81	14.50	29.66	21.51	4.15	6.81	1.28
114	ER17a	ExonRegion	0	159.42	238.50	133.69	507.62	148.23	463.31	93.56
115	E17a_E18a	KnownJunction	0	145.47	219.24	105.46	428.91	116.76	408.27	71.17
116	ER18a	ExonRegion	0	110.11	189.96	83.10	416.08	111.79	344.56	73.63
117	E18a_E19a	KnownJunction	0	123.69	215.24	71.10	439.93	129.65	422.66	70.41
118	ER19a	ExonRegion	0	126.87	252.04	80.07	504.53	152.38	457.49	88.16
119	E19a_E20a	KnownJunction	0	122.00	291.56	87.93	539.41	156.28	469.75	99.26
120	I19	Intron	1	26.86	10.87	19.20	16.09	2.56	6.20	1.81
121	I19_SR1	SilentIntronRegion	1	27.80	11.41	20.07	16.52	2.64	6.28	1.83
122	ER20a	ExonRegion	0	148.82	283.51	96.38	537.62	170.94	479.92	92.19
123	E20a_E21a	KnownJunction	0	107.73	252.89	85.81	458.03	170.89	427.62	75.38
124	I20	Intron	1	29.96	14.46	15.88	24.68	2.98	12.14	1.44
125	I20_SR1	SilentIntronRegion	1	30.01	14.49	15.91	24.72	2.98	12.16	1.44
126	ER21a	ExonRegion	0	110.93	252.91	76.77	485.57	145.83	459.34	75.41
127	E21_Da	NovelBoundary	1	40.59	11.77	22.36	26.01	2.07	12.81	2.62
128	E21a_E22a	KnownJunction	0	69.75	238.70	62.77	462.63	162.91	442.84	75.37
129	I21	Intron	1	49.49	14.65	28.03	18.99	3.87	9.15	1.87
130	I21_SR1	SilentIntronRegion	1	51.45	13.18	25.15	18.72	3.44	7.23	1.80
131	I21_AR1	ActiveIntronRegion	1	45.65	16.96	28.76	21.78	4.26	10.19	1.85
132	I21_SR2	SilentIntronRegion	1	53.90	13.10	33.90	13.30	4.10	11.67	2.12
133	E22_Aa	NovelBoundary	1	78.41	31.60	35.48	13.82	6.18	18.89	2.64
134	ER22a	ExonRegion	0	109.61	262.53	81.44	501.31	108.28	483.41	64.93
135	E22a_E23a	KnownJunction	0	90.74	244.30	77.84	458.87	132.16	443.05	47.48
136	I22	Intron	1	54.56	13.90	28.25	29.16	2.68	18.93	1.18
137	I22_SR1	SilentIntronRegion	1	62.24	15.20	31.89	32.22	2.78	21.49	1.30
138	I22_AR1	ActiveIntronRegion	1	59.17	14.98	25.59	31.87	2.52	18.25	1.80
139	I22_SR2	SilentIntronRegion	1	20.46	8.31	13.04	15.79	2.33	8.01	0.57
140	E23_Aa	NovelBoundary	1	40.52	18.47	22.17	22.70	1.98	13.64	1.52
141	ER23a	ExonRegion	0	112.60	278.21	111.32	537.66	162.84	521.41	67.96
142	E23a_E24a	KnownJunction	0	74.30	280.61	96.54	447.30	281.73	529.35	72.79
143	E23a_E25a	NovelJunction	1	33.60	27.66	23.29	145.51	2.28	92.11	2.65
144	ER24a	ExonRegion	0	130.36	276.31	144.51	483.11	217.93	579.26	93.39
145	E24a_E25a	KnownJunction	0	149.06	272.28	149.15	511.67	193.57	602.41	94.34
146	E25_Aa	NovelBoundary	1	24.87	5.99	17.36	20.26	0.00	18.33	1.50
147	ER25a	ExonRegion	0	121.88	172.69	114.27	345.47	138.91	385.21	52.41
148	E25_Da	KnownBoundary	0	50.60	17.76	35.02	45.73	44.63	43.84	8.60
149	E25_Db	KnownBoundary	0	33.66	22.93	16.83	48.60	32.37	38.70	9.57
150	ER25b	ExonRegion	1	95.67	46.16	59.95	113.47	83.41	96.85	20.91
151	ER25c	ExonRegion	0	87.81	81.98	63.30	161.21	96.25	170.90	24.34
152	IG19_AR2	ActiveIntergenicRegion	0	5.38	3.64	3.39	8.02	0.00	4.90	0.67
153	IG19_AR3	ActiveIntergenicRegion	0	6.53	3.64	3.39	8.73	0.00	4.90	0.67
154	IG19_AR4	ActiveIntergenicRegion	0	6.08	6.07	2.88	8.62	0.00	4.09	0.00
155	IG19_AR6	ActiveIntergenicRegion	0	9.59	3.36	4.19	9.39	0.09	4.32	0.80