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Series GSE84381 Query DataSets for GSE84381
Status Public on Jul 01, 2017
Title Patterns of host gene expression associated with harboring a foregut microbial community
Organisms Rattus norvegicus; Neotoma stephensi
Experiment type Expression profiling by high throughput sequencing
Summary We compared gene expression in the foregut tissues of two rodent species: Stephen's woodrat (Neotoma stephensi), which harbors a dense foregut microbial community, and the lab rat (Rattus norvegicus), which lacks such a community. We found that woodrats have higher abundances of transcripts associated with smooth muscle processes, specifically a higher expression of the smoothelin-like 1 gene, which may assist in contractile properties of this tissue to retain food material in the foregut chamber. The expression of genes associated with keratinization and cornification exhibited a complex pattern of differences between the two species, suggesting distinct molecular mechanisms for this process in each of the two species. Lab rats exhibited higher abundances of transcripts associated with immune function, likely to inhibit microbial growth in the foregut of this species. Some of our results were consistent with previous findings in ruminants (high expression of facilitative glucose transporters, lower expression of B4galnt2), suggestive of possible convergent evolution, while other results were unclear, and perhaps represent novel host-microbe interactions in rodents. Overall, our results suggest that harboring a foregut microbiota is associated with changes to the functions and host-microbe interactions of the foregut tissues.
 
Overall design Foregut tissue, polyA-containing mRNA profiles of Stephens' woodrats (Neotoma stephensi) and Sprague Dawley lab rats generated by deep sequencing, in triplicate, using the Illumina HiSeq 2000 platform.
 
Contributor(s) Weiss RB, Kohl KD, Dearing MD
Citation(s) 28874116
Submission date Jul 13, 2016
Last update date May 15, 2019
Contact name Robert B Weiss
E-mail(s) bob.weiss@genetics.utah.edu
Phone (801) 585-5606
Organization name University of Utah
Department Human Genetics
Lab EIHG, Rm 2260B
Street address 15 N 2030 E
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platforms (2)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
GPL22154 Illumina HiSeq 2000 (Neotoma stephensi)
Samples (6)
GSM2232847 N. stephensi replicate 1
GSM2232848 N. stephensi replicate 2
GSM2232849 N. stephensi replicate 3
Relations
BioProject PRJNA329014
SRA SRP078462

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE84381_RAW.tar 950.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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