Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis in multiple sclerosis

ABSTRACT: To address the differential response of the CNS, proteomics was applied in experimental autoimmune encephalomyelitis (EAE) mice and cuprizone (CPZ) mice in two different CNS regions

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Laura Lopez-Mascaraque

PROVIDER: PXD037019 | JPOST Repository | Wed Sep 27 00:00:00 BST 2023

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic changes in amygdala and cortex of fear-conditioned and ErbB4 Knock-out mice

Project description:Chromatin accessibility provides an important window into the regulation of gene expression. Recently, the Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) was developed to profile genome-wide chromatin accessibility. Here we applied a read-downsampling approach to call robust ATAC-seq peaks in order to profile the regions of differential chromatin accessibility of central amygdala and cortex between different experimental conditions; fear-conditioned vs. control mice and ErbB4 knock-out vs. wild-type mice.

2019-02-21 | GSE111021 | GEO

Rattus norvegicus

Project description:Transcript Profiling of Different CNS Regions in Response to Experimental Restraint Stress on Rats

| PRJNA118893 | ENA

Sex Differences in the Neuronal Transcriptome and Synaptic Mitochondrial Function in Cerebral Cortex of a Multiple Sclerosis Model

Project description:Multiple sclerosis (MS) affects the cerebral cortex, inducing cortical atrophy and neuronal and synaptic pathology. Despite the fact that women are more susceptible to getting MS, men with MS have worse disability progression. Here, we address sex differences in neurodegenerative mechanisms focusing on the cerebral cortex using the MS model, chronic experimental autoimmune encephalomyelitis (EAE). RNA sequencing of neurons in cerebral cortex during EAE showed robust differential gene expression in male EAE mice compared to male healthy, age-matched, control mice. In contrast, there were few differences in female EAE mice compared to female controls. The most enriched differential gene expression pathways in male mice during EAE were mitochondrial dysfunction and oxidative phosphorylation. Mitochondrial morphology showed significant abnormalities in the cerebral cortex of EAE males, but not EAE females. Regarding function, synaptosomes isolated from cerebral cortex of male EAE mice demonstrated decreased oxygen consumption rates during respirometry assays. Together, cortical neuronal transcriptomics, mitochondrial morphology, and functional respirometry assays in synaptosomes revealed worse neurodegeneration in male EAE mice. This is consistent with worse neurodegeneration in MS men and reveals a model and a target to develop treatments to prevent cortical neurodegeneration and mitigate disability progression in MS men.

2023-11-13 | GSE239455 | GEO

Whole transcriptome bisufilte sequencing for multiple species [Drosophila]

Project description:We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species.

2022-02-27 | GSE127776 | GEO

Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]

Project description:We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species.

2022-02-27 | GSE127779 | GEO

GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells

Project description:Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link chromatin accessibility with genotype in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factors motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors towards a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.

2023-05-04 | GSE214812 | GEO

Nanopore long-read RNA sequencing shows region-specific sex differences in wild-type mouse brain mRNA isoform expression and usage

Project description:To address differences in splicing across brain regions (cerebellum, cortex, hippocampus, and striatum) and sexes, we used long-read Oxford Nanopore Technologies (ONT) RNA sequencing to sequence 40 wild-type mouse brain cDNA libraries from 10 mice and calculated differential expression and transcript usage. We found that there is differential gene expression, differential transcript expression, and differential transcript usage across all brain regions. We found that the brain region with the most differential expression and transcript usage is the cerebellum, potentially driven by differences in cell type composition. Additionally, our findings suggest there is much differential splicing across brain regions and to a lesser extent, within brain regions across sexes.

2024-01-31 | GSE246705 | GEO

Whole transcriptome bisufilte sequencing for multiple species [Xenopus tropicalis]

Project description:We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species.

2022-02-27 | GSE127778 | GEO

Whole transcriptome bisufilte sequencing for multiple species [Xenopus laevis]

Project description:We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species.

2022-02-27 | GSE127777 | GEO

Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Project description:The aim of this BBSRC-funded project is to develop laser-capture microdissection (LCMD) to isolate small cell clusters in different regions of arabidopsis embryos at different stages of development; to develop RNA amplification procedures on dissected tissue sampes; and to use DNA microarray techniques to investigate global transcriptional differences between samples. Cryosectioned embryos of ecotype Col-O of globular, heart and torpedo stage were used to isolate cell clusters from the apical and basal regions, for RNA isolation and amplification. !Samples will be provided as T7-primed cDNA, with three biological replicates for each tissue to be analysed. Each replicate comprises cDNA from pooled tissue samples from ca. 15 embryos. The experimental details have been discussed with Sean May et al. at NASC. Experimenter name = Stuart Casson and Matthew Spencer Experimenter phone = 0191 374 7356 Experimenter fax = 0191 374 2417 Experimenter institute = Durham University Experimenter address = Integrative Cell Biology Laboratory Experimenter address = School of Biological Sciences Experimenter address = Durham University Experimenter address = South Road Experimenter address = Durham Experimenter zip/postal_code = DH1 3LE Experimenter country = UK Keywords: organism_part_comparison_design; development_or_differentiation_design

2007-01-08 | GSE5730 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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