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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
MetabolomicsRapid UHPLC-MS metabolite profiling and phenotypic assays reveal genotypic impacts of nitrogen supplementation in oats
INTRODUCTION: Oats (Avena sativa L.) are a whole grain cereal recognised for their health benefits and which are cultivated largely in temperate regions providing both a source of food for humans and animals, as well as being used in cosmetics and as a potential treatment for a number of...
2020-06-11 | MTBLS804 | MetaboLights
GenomicsDTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV
DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase Pol IV transcribes target sequences to initiate 24-nt siRNA produ...
ORGANISM(S): Arabidopsis thaliana 
2013-06-03 | E-GEOD-44209 | biostudies-arrayexpress
TranscriptomicsIBM1, a JmjC domain histone demethylase, is involved in the regulation of RNA-directed DNA methylation through epigenetic control of RDR2 and DCL3 expression in Arabidopsis.
The small RNA mediated DNA methylation (RdDM) is highly elaborated in Arabidopsis as an important epigenetic pathway controls expression of genes and multiple developmental processes. RDR2 and DCL3 are necessary factors to the 24-nt siRNA biogenesis and the RdDM pathway. Here, we find that IBM1 (inc...
ORGANISM(S): Arabidopsis thaliana 
2012-08-03 | E-GEOD-32284 | biostudies-arrayexpress
MetabolomicsApplication of HPLC-PDA-MS metabolite profiling to investigate the effect of growth temperature and day length on blackcurrant fruit
INTRODUCTION: Blackcurrant (Ribes nigrum L.) is an excellent example of a “super fruit” with potential health benefits. Both genotype and cultivation environment are known to affect the chemical composition of blackcurrant, especially ascorbic acid and various phenolic compounds. Environmental condi...
2019-02-12 | MTBLS773 | MetaboLights
TranscriptomicsThe SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [mRNA-Seq]
DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: MET1, CMT3, DRM2, and CMT2. However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families an...
ORGANISM(S): Arabidopsis thaliana 
2014-11-25 | E-GEOD-62799 | biostudies-arrayexpress
ProteomicsCysteine-directed isobaric labeling combined with GeLC-FAIMS MS for quantitative top-down proteomics
The quantification of proteoforms, i.e., all molecular forms in which proteins can be present, by top-down proteomics provides essential insights into biological processes at the molecular level. Isobaric labeling-based quantification strategies are suitable for multi-dimensional separation strategi...
ORGANISM(S): Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2025-05-07 | PXD055510 | Pride
Top-down proteomics  tmt labeling  quantitative proteomics  faims  gelc  peppi 
TranscriptomicsTranscription profiling of Arabidopsis dms4-1, drd1-1 and drd1-6 mutant seedlings against wild-type to identify targets of IWR1-like transcription factor
We identified in a forward genetic screen a novel factor required for RNA-directed DNA methylation (IWR1-like transcription factor). The aim of the study was to identify natural targets of this factor and to compare it to targets of drd1 another major key factor required for the RNA silencing proces...
ORGANISM(S): Arabidopsis thaliana 
2010-01-10 | E-MEXP-2251 | biostudies-arrayexpress
TranscriptomicsDNA Topoisomerase 1a Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [RNA-Seq]
RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found th...
ORGANISM(S): Arabidopsis thaliana 
2014-07-08 | E-GEOD-50719 | biostudies-arrayexpress
UnknownSpatially-directed protein identification from tissue sections by top-down LC-MS/MS with electron transfer dissociation.
Not available
S-EPMC3749783 | biostudies-literature
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