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

Eckalbar et al.

Eckalbar et al. BMC Genomics 2013 14:49   doi:10.1186/1471-2164-14-49

Open Data