Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacteroides thetaiotaomicron VPI-5482

ABSTRACT: Tnseq of B. thetaiotaomicron

PROVIDER: PRJNA846511 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19576036.fastq.gz	Fastqsanger.gz
	SRR19576037.fastq.gz	Fastqsanger.gz
	SRR19576038.fastq.gz	Fastqsanger.gz
	SRR19576039.fastq.gz	Fastqsanger.gz
	SRR19576040.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

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

Bacteroides thetaiotaomicron VPI-5482

Project description:Bacteroides thetaiotaomicron VPI-5482 Raw sequence reads

| PRJNA540869 | ENA

Bacteroides thetaiotaomicron VPI-5482

Project description:Bacteroides thetaiotaomicron VPI-5482 Transcriptome or Gene expression

| PRJNA397082 | ENA

Bacteroides thetaiotaomicron VPI-5482

Project description:Strain engineering identifies unstable genetic loci in Bacteroides thetaiotaomicron

| PRJNA778765 | ENA

Bacteroides thetaiotaomicron VPI-5482

Project description:Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization

| PRJNA797447 | ENA

Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 grown on ribose

Project description:Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 grown on ribose to look at global changes in regulation in vitro on the defined monosaccharide, ribose as a sole carbon source. Methods: Bacteroides thetaiotaomicron was grown on 5 mg/ml ribose or glucose as a sole carbon source in vitro. Fold change was calculated as ribose over glucose with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.6-0.8), 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 RPKM 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 RPKM expression level in either glucose or ribose, and a p-value < 0.05 (t test with Benjamini-Hochberg correction) Results: We identified 81 genes differentially expressed at a 5-fold cutoff when grown in ribose over the reference glucose condition, many of which are involved in other metabolic processes important for seemingly unrealted nutrients.

2020-01-01 | GSE137571 | GEO

Bacteroides thetaiotaomicron VPI-5482

Project description:Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

| PRJNA168084 | ENA

Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482

2013-05-29 | GSE47418 | GEO

Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482

Project description:Regulation of EHEC gene expression by the gut commensal bacterium B. thetaiotaomicron. EHEC is a human pathogen that colonizes in the colon where B. thetaiotaomicron is a predominant commensal. We used microarrays to evaluate global regulation of EHEC when cultured with B. thetaiotaomicron. EHEC and B. thetaiotaomicron were co-cultured in vitro under strict anaerobic conditions in low-glucose Dulbecco's modified Eagle's medium (DMEM). Total RNA from bacteria grown to mid-logarithmic phase was extracted and hybridized to an Affymetrix E. coli 2.0 gene chip according to manufacturer's specifications: http//www.affymetrix.com/support/technical/manual/expression_manual.affx

2013-05-29 | E-GEOD-47418 | biostudies-arrayexpress

Bacteroides thetaiotaomicron VPI-5482

Project description:Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont

| PRJNA111713 | ENA