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Series GSE149357 Query DataSets for GSE149357
Status Public on Sep 01, 2020
Title RNA-seq of human gut bacterial isolates grown on seaweed polysaccharides
Organisms Bacteroides thetaiotaomicron; Faecalicatena contorta; Faecalicatena fissicatena; Bacteroides xylanisolvens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source
Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates. 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 with both biological replicates with a normalized expression level >1% of the overall average RPKM expression level. READS WERE ANALYZED .......GABRIEL FILL IN
Results: We identified novel polysaccharide utiilization loci in 5 strains of human gut bacteria
 
Overall design rRNA-depleted, mRNA profiles of human gut bacteria on respective seaweed polysaccharides run on Illumina Hi-Seq platform.
 
Contributor(s) Pudlo NA, Pereira GV, Martens E
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Submission date Apr 26, 2020
Last update date Sep 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 (4)
GPL21072 Illumina HiSeq 2000 (Bacteroides xylanisolvens)
GPL28453 Illumina HiSeq 2000 (Bacteroides thetaiotaomicron)
GPL28454 Illumina NextSeq 500 (Faecalicatena contorta)
Samples (24)
GSM4498559 Bacteroides thetaiotaomicron 3731 Galactose 1
GSM4498560 Bacteroides thetaiotaomicron 3731 Galactose 2
GSM4498561 Bacteroides thetaiotaomicron 3731 Carrageenan 1
Relations
BioProject PRJNA628169
SRA SRP258572

Download family Format
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Supplementary file Size Download File type/resource
GSE149357_Bthetaiotaomicron3731_DEseq.xlsx 447.9 Kb (ftp)(http) XLSX
GSE149357_Bxylanisolvens18002P_DEseq.xlsx 431.2 Kb (ftp)(http) XLSX
GSE149357_Fcontorta548_DEseq.xlsx 499.9 Kb (ftp)(http) XLSX
GSE149357_Fcontorta588_DEseq.xlsx 335.9 Kb (ftp)(http) XLSX
GSE149357_FfissicatenaD5_DEseq.xlsx 473.6 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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