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Data released on February 10, 2017

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

Geng, X; Gou, Q; Li, W; Shang, H; Zhang, F; Zang, X; Zeng, B; Li, J; Wang, Y; Ma, J; Guo, J; Jian, J; Chen, B; Qiao, Z; Zhou, M; Wei, H; 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 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix006

Accessions (data included in GigaDB):

BioProject: PRJNA350354
SRA: SRP092015

Transcriptomic

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Funding:

  • Funding body - National Natural Science Foundation of China
  • Award ID - 31572270
  • Funding body - Major Scientific and Technological Projects of Henan
  • Award ID - 111100910600

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN05938529141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from spinal cord ...
Sex:female
Life stage:adult
...
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SAMN05938530141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from spleen of An...
Sex:female
Life stage:adult
...
+
SAMN05938531141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from stomach of A...
Sex:female
Life stage:adult
...
+
SAMN05938532141262 Chinese giant salamanderAndrias davidianus Description:RNA sample extracted from tail fat of ...
Sex:female
Life stage:adult
...
+
Displaying 21-24 of 24 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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