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MetabolomicsAtlas of one-carbon metabolism in conventional and germ-free mice reveals folate as a key determinant of biochemical pathways

Folates participate in the one-carbon metabolism (OCM) cycle, supporting many biochemical pathways. Existing methods to profile folate are limited in the diversity of vitamers they measure and the samples they profile. We present a metabolomics workflow for stable extraction, separation, and meas...

2026-02-10 | MTBLS13484 | MetaboLights
MetabolomicsBile acid analysis of the germ free mouse gut
Not available
ORGANISM(S): Mus musculus 
ST000831 | MetabolomicsWorkbench
MetabolomicsHarnessing a Germ-Free Mouse Gut Bioreactor for Directed Evolution of Probiotics to Combat NAFLD

The data uploaded in this study were obtained from an interventional experiment in which non-alcoholic fatty liver disease (NAFLD) model mice were treated with either the original or adapted bacterial strains, followed by fecal sample collection and targeted bile acid metabolomic analysis.

2026-01-20 | MTBLS13718 | MetaboLights
MetabolomicsCecal metabolome of gnotobiotic (containing a 14-member synthetic human gut microbiota), and germ-free mice fed with two distinct rodent diets with varying fiber content.
Not available
ORGANISM(S): Mus musculus 
ST002172 | MetabolomicsWorkbench
TranscriptomicsGerm-free and anti-biotic treated rats
The objective of the study was identify hepatic genes with expression by deprivation of gut flora. Two models were used: model 1 (study 1443KR) examined germ-free Sprague Dawley and model 2 (1512KR) examined antibiotic treated Han Wistar rats. Germ-free vs. non-germ-free, antibiotic treated vs. untr...
ORGANISM(S): Rattus norvegicus 
2010-08-31 | E-GEOD-21937 | biostudies-arrayexpress
ProteomicsDevelopment of a Mass Spectrometry-Based Quantitation Assay for Human Body Fluid Proteins using a Wheat Germ Cell-Free Synthesis System
In this study, we have developed a large-scale SRM assay targeting human body fluid proteins based on publicly available proteomics data. We first aimed to produce, in a high throughput manner, a peptide reference library. For this purpose, we selected 2,201 targeted peptides representing 1,215 prot...
ORGANISM(S): Homo sapiens (Human) 
2016-05-24 | PXD002090 | Pride
Wheat germ cell-free system Human body fluid proteins Targeted proteomics Reference peptide library 
GenomicsTissue neutrophil heterogeneity in germ free mice
Tissue neutrophil heterogeneity in germ free mice
PRJNA597017 | ENA
TranscriptomicsTranscription profiling of mouse laser captured small intestine isolated fom normal and germ free animals
This study delineated how small intestinal resident microflora impact gene expression in Paneth cells. Experiment Overall Design: Paneth cells were isolated by laser capture microdissection from the small intestines of germ-free and conventionalized (10 day) mice. RNAs from 3 mice per group were po...
ORGANISM(S): Mus musculus 
2008-06-13 | E-GEOD-5156 | biostudies-arrayexpress
TranscriptomicsRNA-seq of fetal murine intestine, brain and placenta from germ-free vs specific pathogen free dams
The effects of maternal microbiota on the fetal development was investigated by comparing tissues of fetuses from germ-free (GF) and normal (SPF) murine dams using RNA-seq and non-targeted metabolomics (for metabolomics data, see: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02...
ORGANISM(S): Mus musculus 
2022-12-17 | E-MTAB-12442 | biostudies-arrayexpress
TranscriptomicsGlobal hepatic gene expression data from germ free and specific pathogen free male mice.
Liver clock regulates transcription of hepatic genes in response to feeding. To explore the possibility that the microbiome influences this process, we measured the liver transcriptome in normal mice (Specific Pathogen Free or SPF mice) and compared it to the transcriptome in mice lacking microbiota...
ORGANISM(S): Mus musculus 
2016-02-20 | E-GEOD-71628 | biostudies-arrayexpress
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