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Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

ABSTRACT: Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

PROVIDER: PRJNA715915 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14017863_1.fastq.gz	Fastqsanger.gz
	SRR14017863_2.fastq.gz	Fastqsanger.gz
	SRR14017864_1.fastq.gz	Fastqsanger.gz
	SRR14017864_2.fastq.gz	Fastqsanger.gz
	SRR14017865_1.fastq.gz	Fastqsanger.gz

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Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

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

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

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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.

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

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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).

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