Table 1.
Overview of de novo transcript assembly for A. carolinensis based on RNA-Seq data from 14 adult and embryonic tissues and deposited EST sequence data
| De novo RNA-Seq | # Reads | De novo assembled transcripts | Transcripts aligning to Anocar2.0 assembly | PASA assembled transcripts |
|---|---|---|---|---|
| Embryo-28 somite stage |
52,548,024 |
83,627 |
81,032 |
22,670 |
| Embryo-38 somite stage |
55,048,179 |
99,578 |
95,753 |
24,595 |
| Regenerating tail tip |
122,099,352 |
92,275 |
88,150 |
22,278 |
| Regenerating tail base |
31,721,054 |
78,005 |
73,516 |
24,897 |
| Original tail |
109,404,060 |
96,450 |
91,601 |
20,240 |
| Adrenal |
55,858,836 |
110,349 |
101,449 |
20,482 |
| Brain |
32,518,977 |
203,519 |
192,407 |
33,912 |
| Dewlap skin |
31,785,178 |
81,598 |
76,866 |
25,853 |
| Embryos (pooled) |
59,681,427 |
118,949 |
110,124 |
19,969 |
| Heart |
34,068,834 |
154,255 |
144,617 |
26,582 |
| Liver |
50,782,350 |
89,010 |
81,441 |
21,549 |
| Lung |
48,723,049 |
272,071 |
255,035 |
37,985 |
| Ovary |
35,139,647 |
80,306 |
75,807 |
26,827 |
| Skeletal Muscle |
42,707,477 |
75,006 |
69,250 |
18,857 |
|
Total |
762,086,444 |
1,634,998 |
1,537,048 |
346,696 |
|
EST Library (NCBI) |
# Sequences |
NCBI defined UniGene groups |
Transcripts aligning to Anocar2.0 assembly |
PASA assembled transcripts |
| Brain |
19,139 |
5,631 |
9,991 |
1,715 |
| Dewlap skin |
19,809 |
5,453 |
10,180 |
2,216 |
| Embryo |
38,923 |
8,714 |
9,991 |
4,158 |
| Mixed Organ |
19,863 |
5,657 |
9,327 |
2,053 |
| Ovary |
19,410 |
5,467 |
7,394 |
3,737 |
| Regenerating Tail |
19,851 |
6,751 |
11,064 |
6,757 |
| Testis |
19,807 |
4,261 |
8,677 |
2,594 |
| Total | 156,802 | 41,934 | 66,624 | 23,230 |