Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Bacteroides thetaiotaomicron and burger ingredients

ABSTRACT: Culture of Bacteroides thetaiotaomicron VPI-5482 NCBI:txid818 (Zengler Lab UCSD) in PSB enriched with burger ingredient extracts. Culture performed under anaerobic conditions followed by SPE C18 extraction for LC-MS/MS.Data was acquired in positive ion mode

INSTRUMENT(S): Q Exactive|MS:1001911

ORGANISM(S): 818|bacteroides Thetaiotaomicron

SUBMITTER: Hosein Mohimani Pieter C Dorrestein

PROVIDER: MSV000087685 | GNPS | Tue Jun 22 14:25:00 BST 2021

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - Bacteroides thetaiotaomicron

Project description:Time-course pilot culture of Bacteroides thetaiotaomicron VPI-5482 NCBI:txid818 (Zengler Lab UCSD) in diluted BHI enriched with chemical compounds under anaerobic conditions. Data was acquired in positive ion mode.

2021-03-30 | MSV000087130 | GNPS

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

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

Characterizing the interactions between a naturally-primed IgA (mAb 260.8) and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice [array]

Project description:Comparisons of gnotobiotic Rag1-/- mice, with and without subcutaneous 260.8 hybridomas, disclosed that this IgA does not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but does affect bacterial gene expression in ways that are emblematic of a diminished host innate immune response. C57BL/6 wildtype, C57BL/6J Rag1-/- , and C57BL/6J Rag1-/- mice harboring the 260.8 IgA producing hybridoma were colonized for 10 days with Bacteroides thetaiotaomicron VPI-5482.

2015-06-29 | E-GEOD-65455 | biostudies-arrayexpress

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

High-resolution view at the coding transcriptome and noncoding RNAs of major gut microbe Bacteroides thetaiotaomicron

Project description:Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). Our screen identified ~4,500 TSSs and we globally determined untranslated regions (UTRs), operon structures, and promoter motifs. In addition, dRNA-seq led to the discovery of ~250 noncoding RNA elements, including 124 novel intergenic small RNAs (sRNAs), several of which we validated experimentally. One of them is the conserved, 145 nt-long sRNA BTnc035, that was highly expressed when B. thetaiotaomicron was grown in the presence of N-acetylglucosamine or glucuronic acid as the sole carbon source. Combining computational predictions with experimental data, we determined the secondary structure of BTnc035 and identified target genes of this sRNA. The emerging model places BTnc035 at the center of a metabolic feedback-loop, wherein sensing of N-acetyl-D-glucosamine and D-glucuronic acid induces BTnc035, which in turn may contribute to a metabolic switch from polysaccharide biosynthesis to break-down. Together, we compiled a single-nucleotide resolution transcriptome map of B. thetaiotaomicron and provide the first global analysis of noncoding RNAs in this important anaerobic model bacterium. To allow easy interrogation of our transcriptome data, we developed Theta-Base – an intuitive online browser that can be freely accessed at https://www.helmholtz-hiri.de/en/bacteroides.

2020-06-11 | GSE144492 | GEO

Analysis of the transcriptome of Bacteroides thetaiotaomicron during growth on complex N-glycan as the sole carbon source

Project description:The goal of this project was to sequence the transcriptome of wild type Bacteroides thetaiotaomicron VPI-5482 grown in minimal media with either glucose or bovine alpha 1 acid glycoprotein (AAGP) as the sole carbon source. Using these data we could then compare relative gene expression levels under each condition and identify genes specifically upregulated during growth on AAGP. Analysis of the spent media indicated that only the N-glycan component of the AAGP had been used by the cells to support growth.

2019-04-26 | GSE129572 | GEO

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

Project description:We used Affymetrix GeneChips to determine the physiological differences between biofilm and planktonic cells of Bacteroides thetaiotaomicron strain VPI-5482 (ATCC 29148) by comparing gene expression. For this purpose, B. thetaiotaomicron cells were grown in sterile, continuous flow bioreactors fed with tryptone, yeast extract, glucose (TYG) medium. The bioreactors were controlled at a temperature of 37C using a water jacket and a recirculating water heater. After 8 hours post-inoculation, planktonic cells were harvested from the bulk solution in the bioreactor, and after 8 days post-inoculation, the biofilm was scraped from the carbon paper. RNA was harvested from both biofilm and planktonic populations. RNA was extracted by a phenol:chloroform method and purified with a Qiagen RNA Easy mini-kit. Overall growth conditions are summarized above. The experimental conditions were: biofilm (BF), and planktonic (PL).

2014-01-01 | E-GEOD-38534 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data