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Data released on May 02, 2018

A gene catalogue of the Sprague-Dawley rat gut metagenome

Pan, H; Guo, R; Zhu, J; Wang, Q; Ju, Y; Xie, Y; Zheng, Y; Wang, Z; Li, T; Liu, Z; Lu, L; Li, F; Tong, B; Xiao, L; Xu, X; Li, R; Yuan, Z; Yang, H; Wang, J; Kristiansen, K; Jia, H; Liu, L (2018): A gene catalogue of the Sprague-Dawley rat gut metagenome GigaScience Database. http://dx.doi.org/10.5524/100440 RIS BibTeX Text

Laboratory rats such as the Sprague-Dawley (SD) rats are important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report on the first catalog of microbial genes in fecal samples from Sprague-Dawley rats. The catalog was established using 98 fecal samples from 49 SD rats divided in 7 experimental groups collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 base pairs (BP), among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8% and 31% of the genes could be annotated to KEGG orthologous groups (KOs), modules and pathways, respectively. A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. 97% of the functional pathways in the human catalog were present in the rat catalogue underscoring the potential use of rats for biomedical research.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJEB22973

Keywords:

rat gene catalog metagenomics rheumatoid arthritis 

Metagenomic

http://gigadb.org/images/data/cropped/100440.jpg

Funding:

  • Funding body - Macau Technology Development Fund
  • Award ID - 102/2016/A3
  • Awardee - L Liu
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JSGG20160229172752028
  • Awardee - H Jia
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JCYJ20160229172757249
  • Awardee - H Jia
  • Funding body - National Natural Science Foundation of China
  • Award ID - 81670606
  • Awardee - L Xiao

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
10-11436733  rat gut metagenome Description:Model group, time point 1
Alternative accession-SRA Sample:ERS1971133
Alternative names:10A_RSZYD16111225
...
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10-51436733  rat gut metagenome Description:Model group, time point 5
Alternative accession-SRA Sample:ERS1971329
Alternative names:206A_RSZYD16111274
...
+
1-11436733  rat gut metagenome Description:Normal group, time point 1
Alternative accession-SRA Sample:ERS1971124
Alternative names:1A_RSZYD16111216
...
+
11-11436733  rat gut metagenome Description:Model group, time point 1
Alternative accession-SRA Sample:ERS1971134
Alternative names:11A_RSZYD16111226
...
+
11-51436733  rat gut metagenome Description:Model group, time point 5
Alternative accession-SRA Sample:ERS1971330
Alternative names:207A_RSZYD16111275
...
+
12-11436733  rat gut metagenome Description:Model group, time point 1
Alternative accession-SRA Sample:ERS1971135
Alternative names:12A_RSZYD16111227
...
+
12-51436733  rat gut metagenome Description:Model group, time point 5
Alternative accession-SRA Sample:ERS1971331
Alternative names:208A_RSZYD16111276
...
+
13-11436733  rat gut metagenome Description:Model group, time point 1
Alternative accession-SRA Sample:ERS1971136
Alternative names:13A_RSZYD16111228
...
+
13-51436733  rat gut metagenome Description:Model group, time point 5
Alternative accession-SRA Sample:ERS1971332
Alternative names:209A_RSZYD16111277
...
+
14-11436733  rat gut metagenome Description:Model group, time point 1
Alternative accession-SRA Sample:ERS1971137
Alternative names:14A_RSZYD16111229
...
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Displaying 1-10 of 98 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence assemblyUNKNOWN79.58 MB2018-04-24
Sequence assemblyUNKNOWN100.27 MB2018-04-24
Sequence assemblyUNKNOWN79.05 MB2018-04-24
Sequence assemblyUNKNOWN100.25 MB2018-04-24
Sequence assemblyUNKNOWN90.1 MB2018-04-24
Sequence assemblyUNKNOWN67.61 MB2018-04-24
Sequence assemblyUNKNOWN69.8 MB2018-04-24
Sequence assemblyUNKNOWN76.04 MB2018-04-24
Sequence assemblyUNKNOWN65.98 MB2018-04-24
Sequence assemblyUNKNOWN66.58 MB2018-04-24
Displaying 1-10 of 111 File(s).

History:

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