Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolomics of mouse cerebral cortical brain tissues comparing GF and CONV-R mice

ABSTRACT: Using high coverage metabolomics, we profiled feces, blood sera and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three sample matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera and 58 for brain tissues with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters.

ORGANISM(S): Mouse Mus Musculus

TISSUE(S): Brain

SUBMITTER: Yunjia Lai

PROVIDER: ST001758 | MetabolomicsWorkbench | Wed Apr 28 00:00:00 BST 2021

REPOSITORIES: MetabolomicsWorkbench

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	mwtab	Other

Items per page:

1 - 1 of 1

Similar Datasets

Metabolomics of mouse feces comparing GF and CONV-R mice

Project description:Using high coverage metabolomics, we profiled feces, blood sera and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three sample matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera and 58 for brain tissues with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters.

2021-04-26 | ST001756 | MetabolomicsWorkbench

Metabolomics of mouse blood sera comparing GF and CONV-R mice

2021-04-28 | ST001757 | MetabolomicsWorkbench

Cell-to-cell adhesion and neurogenesis in human cortical development: a study comparing 2D monolayers with 3D organoid cultures

Project description:Organoids (ORG) are increasingly used as models of cerebral cortical development. Here we compared transcriptome and cellular phenotypes between ORG and monolayers (MON) generated in parallel from three biologically distinct iPSC lines. Multiple read-outs revealed increased proliferation in MON, which was caused by increased integrin signaling. MON also exhibited altered radial glia polarity, global suppression of Notch signaling and impaired generation of intermediate progenitors (INP), outer radial glia (oRG) and cortical neurons, which were all partially reversed by reaggregation of dissociated cells into organoids. Network analyses revealed co-clustering of cell adhesion, Notch- related transcripts their transcriptional regulators in a module strongly downregulated in MON. The data suggest that cortical ORG, with respect to MON, initiates more efficient Notch signaling in ventricular radial glia owing to preserved cell adhesion, resulting in subsequent generation of INP and oRG, in a sequence that better recapitulates the evolution of the cortical ontogenetic process.

2020-01-01 | GSE134216 | GEO

Expression data from Germ-Free (GF) and L.NK2-colonized mice intestinal epithelial cells and Peyer's patches cells

Project description:Lactobacillus NK2 (L.NK2) is a commensal microbe, isolated from the mouse intestinal feces in our lab. To examine the potential role of L. NK2 in the gut immunity, we monocolonized GF mice with L.NK2. And, we conducted a microarray experiment to compare the transcriptomes of GF and L.NK2-colonized mice intestines under the same experimental condition We used microarrays to detail the global programme of gene expression in intestinal epithelial cells (IEC) and Peyer's patches cells (PP) of GF and L.NK2-colonized mice.

2018-03-01 | GSE111111 | GEO

Expression data from Germ-Free (GF) and L.NK318.1-colonized (NK318.1) mice intestinal epithelial cells and Peyer's patches cells

Project description:Lactobacillus NK318.1 is a commensal microbe isolated from the mouse intestinal feces in our lab. To examined the potential role of L. NK318.1 in the gut immunity, we monocolonized GF mice with L.NK318.1. And, we conducted a microarray experiment to compare the transcriptomes of GF and NK318.1 mice intestines under the same experimental condition We used microarrays to detail the global programme of gene expression in intestinal epithelial cells (IEC) and Peyer's patches cells (PP) of GF and NK318.1 mice.

2017-05-12 | GSE98819 | GEO

Distal ileal antibiotic infusion affects the expressions of neurotransmitters in the hypothalamus of piglets

Project description:Purpose: Gut microbiota-brain axis serves as an emerging pathway affecting brain function. Hindgut has a higher proportion of microbes than foregut, however whether alteration in hindgut microbiota is related to brain functional change remains unclear. The present study used antibiotics to modulate the hindgut microbiota, to investigate the changes in the functions of porcine hypothalamus. Methods: Twelve piglets (12.08 ± 0.28 kg) fitted with T-cannula at the distal ileum were fed a standard diet and randomly assigned to two groups (n=6) for ileal infusions of saline (control group) and an antibiotic mix (ampicillin, gentamycin and metronidazole; antibiotic group), respectively. After the 25-day experiment, the microbiota and metabolites in feces, concentrations of amino acids and neurotransmitters in hypothalamus and blood, and transcriptomics profiles of hypothalamus were analyzed. Results: The results showed that the antibiotic infusion resulted in an increase in aromatic amino acids (AAA)-utilizing genera, notably Lactobacillus, and a decrease in the concentrations of AAAs including tryptophan, tyrosine and phenylalanine in feces. Correspondingly, concentrations of AAAs in the blood and hypothalamus also decreased. In the hypothalamus, the concentrations of AAAs related neurotransmitters 5-HT and dopamine decreased. Meanwhile, the compensatory upregulations of neurotransmitter transporter genes such as SERT, DAT and synthesis-related genes TPH2 and AADC were observed (adjusted P < 0.001). Furthermore, the concentrations of 5-HT and dopamine decreased in the blood. Conclusion: In conclusion, the results revealed that the ileal antibiotic infusion could affect the expressions of neurotransmitters in the porcine hypothalamus. The changes of hindgut microbial composition, circulating AAA profile and hypothalamic neurotransmitter expressions indirectly suggested that the hindgut microbiota may affect the brain functions.

2018-12-20 | GSE97738 | GEO

Dissecting developmental disorders caused by CTCF mutation at R567 [RNA-seq]

Project description:In this study, we analyzed gene expression change in brain tissues, in vitro cultured neurons and cortical organoids by using RNA-seq.

2024-05-06 | GSE214689 | GEO

A Learning-Enhanced Two-Pair Spatiotemporal Reflectance Fusion Model for GF-2 and GF-1 WFV Satellite Data.

Project description:Since requirements of related applications for time series remotely-sensed images with high spatial resolution have been hard to be satisfied under current observation conditions of satellite sensors, it is key to reconstruct high-resolution images at specified dates. As an effective data reconstruction technique, spatiotemporal fusion can be used to generate time series land surface parameters with a clear geophysical significance. In this study, an improved fusion model based on the Sparse Representation-Based Spatiotemporal Reflectance Fusion Model (SPSTFM) is developed and assessed with reflectance data from Gaofen-2 Multi-Spectral (GF-2 MS) and Gaofen-1 Wide-Field-View (GF-1 WFV). By introducing a spatially enhanced training method to dictionary training and sparse coding processes, the developed fusion framework is expected to promote the description of high-resolution and low-resolution overcomplete dictionaries. Assessment indices including Average Absolute Deviation (AAD), Root-Mean-Square Error (RMSE), Peak Signal to Noise Ratio (PSNR), Correlation Coefficient (CC), spectral angle mapper (SAM), structure similarity (SSIM) and Erreur Relative Global Adimensionnelle de Synthèse (ERGAS) are then used to test employed fusion methods for a parallel comparison. The experimental results show that more accurate prediction of GF-2 MS reflectance than that from the SPSTFM can be obtained and furthermore comparable with popular two-pair based reflectance fusion models like the Spatial and Temporal Adaptive Fusion Model (STARFM) and the Enhanced-STARFM (ESTARFM).

| S-EPMC7146212 | biostudies-literature

Autoantibodies in sera from Sjogren's syndrome mice

Project description:We performed autoantigen arrays on sera derived from Sjogren's syndrome mice that lacked Myd88 systemically (NOD.B10LSL-/- strain) or lacked Myd88 in specific tissues (NOD.B10Myd88delta and NOD.B10LSL-/-Vav+ strains). We also examined sera from Myd88-sufficient controls (NOD.B10Myd88fl/fl, NOD.B10, and NOD.B10LSL+/- strains).

2021-01-25 | GSE163395 | GEO

Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue

Project description:Transposase-accessible chromatin by sequencing (ATAC-seq) has emerged as an advantageous technique to assess chromatin accessibility owing to the robustness of "tagmentation" process and a relatively faster library preparation. A comprehensive ATAC-seq protocol from Drosophila brain tissue is currently unavailable. Here, we have provided a detailed protocol of ATAC-seq assay from Drosophila brain tissue. Starting from dissection and transposition to amplification of libraries has been elaborated. Furthermore, a robust ATAC-seq analysis pipeline has been presented. The protocol can be easily adapted for other soft tissues.

2023-10-24 | GSE246106 | GEO

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