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Series GSE155869 Query DataSets for GSE155869
Status Public on Dec 01, 2020
Title RNA-seq of human gut Bacteroides xylanisolvens and Bacteroides ovatus isolates grown on mucin O-linked glycans compared to glucose
Organisms Bacteroides ovatus; Bacteroides xylanisolvens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Examining the transcriptome of human gut bacteria (Bacteroides xylanisolvens/Bacteroides ovatus) that grow on mucin O-linked glycans as a sole carbon source
Methods: Strains were grown on 10 mg/ml mucin O-linked glycans (MOG) or 5 mg/ml glucose as a sole carbon source in vitro. Fold change was calculated as MOG over glucose. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and biological replicates with a normalized expression level >1% of the overall average RPKM expression level.
Results: We identified genes activated in response to mucin O-linked glycans from Bacteroides xylanisolvens/Bacteroides ovatus strains
 
Overall design rRNA-depleted, mRNA profiles of human gut bacteria grown on mucin O-linked glycans run on Illumina Hi-Seq platform.
 
Contributor(s) Pudlo NA, Urs K, Martens EC
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Submission date Aug 07, 2020
Last update date Dec 01, 2020
Contact name Eric Martens
E-mail(s) emartens@umich.edu
Organization name University of Michigan
Street address 1150 W. Medical Center Dr.
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (2)
GPL21072 Illumina HiSeq 2000 (Bacteroides xylanisolvens)
GPL28983 Illumina HiSeq 2000 (Bacteroides ovatus)
Samples (24)
GSM4714867 Bacteroides xylanisolvens D22 glucose 1
GSM4714868 Bacteroides xylanisolvens D22 glucose 2
GSM4714869 Bacteroides xylanisolvens D22 glucose 3
Relations
BioProject PRJNA655899
SRA SRP276654

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Supplementary file Size Download File type/resource
GSE155869_Bacteroides_ovatus_3-1-23_RNAseq.xlsx 81.5 Kb (ftp)(http) XLSX
GSE155869_Bacteroides_ovatus_D2_RNAseq.xlsx 105.5 Kb (ftp)(http) XLSX
GSE155869_Bacteroides_ovatus_NLAE-zl-H59_RNAseq.xlsx 749.8 Kb (ftp)(http) XLSX
GSE155869_Bacteroides_xylanisolvens_D22_RNAseq.xlsx 85.4 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record
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