Supporting data for "A reference gene set construction using RNA-seq of multiple tissues of Chinese Giant Salamander, Andrias davidianus"

Dataset type: Transcriptomic
Data released on February 10, 2017

Geng X; Li W; Shang H; Gou Q; Zhang F; Zang X; Zeng B; Li J; Wang Y; Ma J; Guo J; Jian J; Chen B; Qiao Z; Zhou M; Wei HJ; Fang X; Xu C (2017): Supporting data for "A reference gene set construction using RNA-seq of multiple tissues of Chinese Giant Salamander, Andrias davidianus" GigaScience Database. http://dx.doi.org/10.5524/100277

DOI10.5524/100277

Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources and its huge (~50 GB) difficult to assemble genome, leads to slow study progression in this field. Here we report the sequenced transcriptome of more than twenty tissues from adult specimens using Illumina Hiseq 2000 technology, and a total of 93,366 non-redundant transcripts with a mean length of 1,326 bp. We for the first time developed an efficient pipeline to construct a high quality reference gene set of CGS and obtained 26,135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6 % of vertebrate universal single-copy orthologs.

Additional details

Read the peer-reviewed publication(s):

Geng, X., Li, W., Shang, H., Gou, Q., Zhang, F., Zang, X., … Xu, C. (2017). A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus. GigaScience, 6(3). doi:10.1093/gigascience/gix006

Accessions (data included in GigaDB):

BioProject: PRJNA350354
SRA: SRP092015





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN05938509141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from abdominal sk...
Sex:female
Life stage:adult
...
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SAMN05938510141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from dorsal skin ...
Sex:female
Life stage:adult
...
+
SAMN05938511141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from lateral skin...
Sex:female
Life stage:adult
...
+
SAMN05938512141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from blood of And...
Sex:female
Life stage:adult
...
+
SAMN05938513141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from brain of And...
Sex:female
Life stage:adult
...
+
SAMN05938514141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from cartilage of...
Sex:female
Life stage:adult
...
+
SAMN05938515141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from eye of Andri...
Sex:female
Life stage:adult
...
+
SAMN05938516141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from fat of Andri...
Sex:female
Life stage:adult
...
+
SAMN05938517141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from fingertip of...
Sex:female
Life stage:adult
...
+
SAMN05938518141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from heart of And...
Sex:female
Life stage:adult
...
+
Displaying 1-10 of 24 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Coding sequenceFASTA31.16 MB2017-02-07
Expression dataCSV25.73 MB2017-02-07
protein sequenceFASTA10.89 MB2017-02-07
transcriptome sequenceFASTA122.13 MB2017-02-07
BLASTTEXT154.29 MB2017-02-07
BLASTTEXT270.37 MB2017-02-07
annotationTEXT4.63 MB2017-02-07
BLASTTEXT115.93 MB2017-02-07
BLASTTEXT36.26 MB2017-02-07
otherTEXT5.66 MB2017-02-07
Displaying 1-10 of 15 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China Cunshuan Xu 31572270
Major Scientific and Technological Projects of Henan Cunshuan Xu 111100910600
Date Action
February 9, 2017 Dataset publish
March 6, 2017 Manuscript Link added : 10.1093/gigascience/gix006