Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In vitro microbiota model recapitulates and predicts individualized sensitivity to dietary emulsifier

ABSTRACT: in vitro microbiota model recapitulates and predicts individualized sensitivity to dietary emulsifier

PROVIDER: PRJEB84075 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Human intestinal microbiome determines individualized inflammatory response to dietary emulsifier carboxymethylcellulose consumption

Project description:Human intestinal microbiome determines individualized inflammatory response to dietary emulsifier carboxymethylcellulose consumption

| PRJEB61305 | ENA

Dietary emulsifier consumption alters gene expression in the amygdala and paraventricular nucleus of the hypothalamus in mice

Project description:Purpose: The goal of the current study was to test whether emulsifier consumption is associated with changes in gene expression in the amygdala and PVN Methods: Adult male C57BL/6J mice received drinking water containing either 1% sodium carboxymethylcellulose (CMC), 1% polysorbate-80 (P80) or water without emulsifier for 12 weeks. PVN and amygdala gene expression was generated by RNA-Seq using an Illumina NextSeq 500. FastQ quality filter was used to filter low quality sequences and Tophat, Bowtie, Cufflinks, and Cuffdiff were used for RNA-Seq analysis. qRT–PCR validation was performed using 6 differential genes of interest. Results: A total of 243 genes were differentially expressed in the amygdala and PVN of emulsifier-treated mice compared to controls. There was minimal overlap of differentially expressed genes in CMC- and P80-treated animals, suggesting that each emulsifier acts via distinct molecular mechanisms to produce an anxiety-like phenotype. Furthermore, gene ontology and pathway analysis revealed that various stress, metabolic, and immune terms and pathways were altered in emulsifier conditions. RNA-seq data was validated with qRT–PCR data (R2= 0.8815). Conclusions: These findings are the first to demonstrate that emulsifier consumption changes gene expression in brain regions that are critical for stress responding, providing possible molecular mechanisms that may underly the observed anxiety-like phenotype

2022-01-27 | GSE194260 | GEO

Individualized microbiotas dictate impact of dietary fibre on colitis sensitivity

Project description:Individualized microbiotas dictate impact of dietary fibre on colitis sensitivity

| PRJEB64164 | ENA

A novel medication decision gene signature predicts response to individualized therapy and prognosis outcomes in hepatocellular carcinoma patients

Project description:Molecular targeted therapy has shown potential in hepatocellular carcinoma (HCC) patients, and immunotherapy applications are developing rapidly. However, clinical guidance for making individualized therapy decisions for HCC patients remains lacking. To facilitate individualized and reasonable clinical guidance for each HCC patient, we constructed the MDH score.

2022-09-22 | GSE213615 | GEO

Dietary emulsifier consumption accelerates type 1 diabetes development in NOD mice

Project description:Dietary emulsifier consumption accelerates type 1 diabetes development in NOD mice

| PRJEB67708 | ENA

Maternal emulsifier consumption programs offspring metabolic and neuropsychological health

Project description:Modern lifestyle is associated with a major consumption of ultra-processed foods (UPF) due to their practicality and palatability. The ingestion of emulsifiers, a main additive in UPFs, has been related to gut inflammation, microbiota dysbiosis, adiposity and obesity. Maternal unbalanced nutritional habits during embryonic and perinatal stages perturb offspring’s long-term metabolic health, thus increasing obesity and associated comorbidity risk. However, whether maternal emulsifier consumption influences developmental programming in the offspring remains unknown. Here we show that, in mice, maternal consumption of dietary emulsifiers (1% CMC and 1% P80 in drinking water), during gestation and lactation, perturbs the development of hypothalamic energy balance regulation centers of the progeny, leads to metabolic impairments, cognition deficits and induces anxiety-like traits in a sex-specific manner. Our findings support the notion that maternal consumption of emulsifiers, common additives of UPFs, causes mild metabolic and neuropsychological malprogramming in the progeny. Our data call for nutritional advice during gestation.

2023-07-31 | GSE231769 | GEO

RNA-seq alignment to individualized genomes

2014-06-10 | GSE45684 | GEO

A novel medication decision gene signature predicts response to individualized therapy and prognosis outcomes in hepatocellular carcinoma patients

Project description:A novel medication decision gene signature predicts response to individualized therapy and prognosis outcomes in hepatocellular carcinoma patients

| PRJNA881935 | ENA

Gene Expression Profiling of Patient-Derived Pancreatic Cancer Xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: Implications to individualized medicine efforts

Project description:c-Myc controls more than 15% of genes responsible for proliferation, differentiation, and cellular metabolism in pancreatic as well as other cancers making this transcription factor a prime target for treating patients. The transcriptome of 55 patient derived xenografts show that 30% of them share an exacerbated expression profile of MYC transcriptional targets (MYC-high). This cohort is characterized by a high level of Ki67 staining, a lower differentiation state and a shorter survival time compared to the MYC-low subgroup. To define classifier expression signature, we selected a group of 10 MYC targets transcripts which expression is increased in the MYC-high group and 6 transcripts increased in the MYC-low group. We validated the ability of these markers panel to identify MYC-high patient-derived xenografts from both: discovery and validation cohorts as well as primary cells cultures from the same patients. We then showed that cells from MYC-high patients are more sensitive to JQ1 treatment compared to MYC-low cells, in both monolayer and 3D cultured spheroids, due to cell cycle arrest followed by apoptosis. Therefore, these results provide new markers and potentially novel therapeutic modalities for distinct subgroups of pancreatic tumors and may find application to the future management of these patients within the setting of individualized medicine clinics.

2017-03-17 | GSE89792 | GEO

RNA-seq alignment to individualized genomes

Project description:The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq. Illumina 100bp single-end liver RNA-seq from 277 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. In addition, Illumina 100bp single-end liver RNA-seq from 128 male 26-week old male mice (20 weeks for NZO strain) from each of the DO founder strains raised on standard chow or high fat diet (8 males per strain by diet group). Each sample was sequenced in 2-4x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.

2014-06-10 | E-GEOD-45684 | 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