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Data released on October 23, 2017

Supporting data for "Comparative transcriptomics of five high-altitude vertebrates and their low-altitude relatives"

Tang, Q; Gu, Y; Zhou, X; Jin, L; Guan, J; Liu, R; Li, J; Long, K; Tian, S; Che, T; Hu, S; Liang, Y; Yang, X; Tao, X; Zhong, Z; Wang, G; Chen, X; Li, D; Ma, J; Wang, X; Mai, M; Jiang, A; Luo, X; Lv, X; Gladyshev, V, N; Li, X; Li, M (2017): Supporting data for "Comparative transcriptomics of five high-altitude vertebrates and their low-altitude relatives" GigaScience Database. http://dx.doi.org/10.5524/100355 RIS BibTeX Text

Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that examined high-altitude adaptation identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown.
We generated a total of 910 Gb high-quality RNA-seq data for 180 samples derived from six tissues of five agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat and yak), and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ~75% reads could be aligned to their respective reference genomes, and on average ~70% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.1. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression, and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes were potentially involved in phenotypic divergence shaped by high-altitude adaptation.
This data serves as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA357880
BioProject: PRJNA362606

Keywords:

high-altitude vertebrates comparative transcriptomics gene expression alternative splicing 

Transcriptomic

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Funding:

  • Funding body - Ministry of Science & Technology of the People's Republic of China
  • Award ID - 2013AA102502
  • Comment - National High Technology Research and Development Program of China (863 Program)
  • Awardee - M Li
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31402046
  • Awardee - Q Tang
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31522055
  • Awardee - M Li
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31601918
  • Awardee - J Ma
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31530073
  • Awardee - X Li
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31472081
  • Awardee - M Li
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 2016NYZ0042
  • Comment - Science & Technology Support Program of Sichuan
  • Awardee - Y Gu
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 2017JQ0011
  • Comment - Youth Science Fund of Sichuan
  • Awardee - Y Gu
  • Funding body - China Postdoctoral Science Foundation
  • Award ID - 2015M572486
  • Awardee - Q Tang
  • Funding body - China Agriculture Research System
  • Award ID - CARS-36
  • Awardee - Y Gu
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 2015TD0012
  • Comment - Program for Innovative Research Team of Sichuan Province
  • Awardee - M Li
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - SCCXTD-005
  • Comment - Program for Pig Industry Technology System Innovation Team of Sichuan Province
  • Awardee - Y Gu
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 15ZA0008
  • Comment - Project of Sichuan Education Department
  • Awardee - X Wang
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 15ZA0003
  • Comment - Project of Sichuan Education Department
  • Awardee - M Li
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 16ZA0025
  • Comment - Project of Sichuan Education Department
  • Awardee - J Ma
  • Funding body - Sichuan Provincial Department of Science and Technology
  • Award ID - 16ZB0037
  • Comment - Project of Sichuan Education Department
  • Awardee - A Jiang

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
H-chicken_heart19031ChickenGallus gallus Description:RNA extracted from heart of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242742
...
+
H-chicken_heart29031ChickenGallus gallus Description:RNA extracted from heart of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242739
...
+
H-chicken_heart39031ChickenGallus gallus Description:RNA extracted from heart of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242736
...
+
H-chicken_kidney19031ChickenGallus gallus Description:RNA extracted from kidney of an adult ...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242620
...
+
H-chicken_kidney29031ChickenGallus gallus Description:RNA extracted from kidney of an adult ...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242619
...
+
H-chicken_kidney39031ChickenGallus gallus Description:RNA extracted from kidney of an adult ...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242618
...
+
H-chicken_liver19031ChickenGallus gallus Description:RNA extracted from liver of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242707
...
+
H-chicken_liver29031ChickenGallus gallus Description:RNA extracted from liver of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242705
...
+
H-chicken_liver39031ChickenGallus gallus Description:RNA extracted from liver of an adult c...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242703
...
+
H-chicken_lung19031ChickenGallus gallus Description:RNA extracted from lung of an adult ch...
Analyte type:RNA
Alternative accession-BioSample:SAMN06242741
...
+
Displaying 1-10 of 187 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 
ScriptPython3.3 KB2017-09-27
ScriptPython3.84 KB2017-09-27
L-cow_heart1 +Expression dataUNKNOWN264.67 KB2017-09-27
L-cow_kidney1 +Expression dataUNKNOWN292.62 KB2017-09-27
L-cow_liver1 +Expression dataUNKNOWN145.95 KB2017-09-27
L-cow_lung1 +Expression dataUNKNOWN506.17 KB2017-09-27
L-cow_muscle1 +Expression dataUNKNOWN394.61 KB2017-09-27
L-cow_spleen1 +Expression dataUNKNOWN371.45 KB2017-09-27
L-chicken_heart1 +Expression dataUNKNOWN217.65 KB2017-09-27
L-chicken_kidney1 +Expression dataUNKNOWN125.56 KB2017-09-27
Displaying 1-10 of 238 File(s).

History:

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