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Transcription analysis of E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774

ABSTRACT: Investigation of whole genome gene expression level changes in E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774 compared to when E. coli is cultured individually.

ORGANISM(S): Escherichia coli O103:H2 str. 12009 Escherichia coli O103:H25

PROVIDER: GSE44790 | GEO | 2014/12/18

SECONDARY ACCESSION(S): PRJNA192719

REPOSITORIES: GEO

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Transcription analysis of E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774

Project description:Investigation of whole genome gene expression level changes in E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774 compared to when E. coli is cultured individually. A study using total RNA recovered from three separate co-cultures (E. coli O103:H25 and B. thetaiotaomicron 1:100) at OD=0.5, compared to when E. coli is cultured individually (5 separate samples including 1-3 technical replicates of each sample). Three separate samples are also recovered when E. coli is cultured in supernatant from Bacteroides thetaiotaomicron at OD=0.5 compared to when E coli is cultured alone. A comparison is also done after treatment with Mitomycin C (MMC). MMC is added at OD=0.5. There are 3 separate samples from each group that are compared (co-culture versus E. coli grown individually, E. coli in supernatant from B. thetaiotaomicron versus E. coli grown individually).

2014-12-18 | E-GEOD-44790 | biostudies-arrayexpress

In vitro transcriptional profiling of Bacteroides thetaiotaomicron in lactose, galactose and human milk oligosaccharides

2013-01-01 | GSE26772 | GEO

In vitro transcriptional profiling of Bacteroides thetaiotaomicron in lactose, galactose and human milk oligosaccharides

Project description:Investigation of the overall in vitro response of Bacteroides thetaiotaomicron to human milk oligosaccharides. Comparison with response to MM-lactose and MM-galactose (Analysis performed using as a baseline datasets GSM301635 and GSM301637 corresponding to Bacteroides thetaiotaomicron response in MM-Glucose) In vitro transcriptional profiles of Bacteroides thetaiotaomicron obtained from biological duplicate cultures taken: (i) at middle log phase in minimal media galactose (MM-Gal) and minimal media lactose (MM-L) and (ii) at two timepoints during log phase in minimal media human milk oligosaccharides (MM-HMO).

2013-01-01 | E-GEOD-26772 | biostudies-arrayexpress

Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [Bacteroides]

Project description:Analysis of the Bacteroides thetaiotaomicron(BT) transcriptome during co-culture with Caco-2 intestinal epithelial cells To identify potential bacterial protein(s) involved in the anti-inflammatory effect of BT in colitis, BT was incubated with Caco-2 human intestinal epithelial cells for 2 hours, and bacterial gene expression was assessed on a Bacteroides thetaiotaomicron VPI-5482 specific microarray. Forty-three BT genes were up-regulated by five-fold or more and of these, twenty genes encoded hypothetical proteins.

2019-03-06 | GSE118525 | GEO

Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 with Bacteroides phage challenge

Project description:Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 challenged with Bacteroides phage to assess surface molecule expression changes Methods: Bacteroides thetaiotaomicron was grown in BPRM in vitro or Germ-Free mice were monocolonized with Bacteroides thetaiotaomicron and gavaged with ARB25 phage. Fold change was calculated as live phage versus heat-killed phage treated samples with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.4-0.5), 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.) using DEseq2 normalization with default parameters. Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average, and a p-value < 0.05 (t test with Benjamini-Hochberg correction) Results: Specific capsule expression was increased in wild-type B. thetaiotaomicron during phage infection in vitro and in vivo. Many corresponding in vivo genes were upregulated as well as other surface layer proteins.

2020-05-01 | GSE147071 | GEO

Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

Project description:Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

2023-03-30 | GSE169260 | GEO

Elucidating BT4338 binding in Bacteroides thetaiotaomicron following 10 minutes of carbon starvation.

Project description:Use ChIPseq to elucidate BT4338 binding in Bacteroides thetaiotaomicron following 10 minutes of carbon starvation.

2019-12-19 | GSE134116 | GEO

Bacteroides thetaiotaomicron

Project description:Bacteroides thetaiotaomicron Genome sequencing

| PRJNA688995 | ENA

Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [mouse colon]

Project description:Analysis of the gut transcriptome as affected by treatment with Bacteroides thetaiotaomicron in a mouse model of IBD Here, we report analysis of the gut transcriptome in IL10KO mice after treatment with Bacteroides thetaiotaomicron (BT). Comparative transcriptome analysis of ascending colon tissue of IL10KO and IL10KO/BT-treated mice showed differential expression of a wide range of genes associated with inflammatory responses between the two treatment groups. Expression of proinflammatory genes and genes involved in pathogen recognition was particularly lower in IL10KO/BT mice.

2019-03-06 | GSE118524 | GEO

Gene expression of Bacteroides thetaiotaomicron, in vivo with and without IgA 225.4

Project description:Rag1-/- C57BL/6 or Rag1-/- C57BL/6 injected with the IgA producing hybridoma producing 225.4 anti- Bacteroides thetaiotaomicron (Capsular polysaccharide 4 dependent carbohydrate epitope specific epitope) mice were colonized with B. thetaiotaomicron wildtype strain VPI-5482 for 10 days. Cecal bacteria were harvested and snap frozen and RNA isolated. Keywords: Single time point, experimental and control groups.

2007-12-27 | GSE9019 | GEO

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