Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-PROT-12

ABSTRACT: Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics

PROVIDER: E-PROT-12 | ExpressionAtlas | 2022-01-14

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-PROT-12 .tsv	Tabular
	E-PROT-12-analysis-methods.tsv	Tabular
	E-PROT-12-configuration.xml	Xml
	E-PROT-12-factors.xml	Xml
	E-PROT-12-zoomifications-log.tsv	Tabular

Items per page:

1 - 5 of 13

Similar Datasets

E-PROT-26

Project description:Deep proteomic profiling of luminal breast cancer progression

2021-05-25 | E-PROT-26 | ExpressionAtlas

SASP signature of beta-cells includes pro-inflammatory and stress response proteins

Project description:To define the senescence-associated secretory phenotype (SASP) of beta-cells, we used conditioned media (CM) generated from bleomycin-treated MIN6 cells and from senescent (beta-Gal-positive) primary beta-cells. In order to culture senescent beta-cells, we isolated islet, FACS-sorted them into beta-Gal-positive and negative populations, excluding immune cells through negative selection of CD45-positive and CD11beta-positive cells. For both the MIN6 and primary beta-cell models, we cultured cells in serum-free media to generate CM for proteomic analysis using the aptamer-based SomaScan platform.

2021-04-06 | GSE150285 | GEO

Using human induced pluripotent stem cells (iPSC) and iPSC-derived neurons to explore cellular phenotypes associated with schizophrenia.

Project description:Schizophrenia and major mental illness are common devastating conditions. Whilst partially effective treatments are available, none are disease-modifying. Notwithstanding important insights provided by animal models there is a need for novel models of mental illness to develop more effective therapies. A study of sporadic schizophrenia-derived human induced pluripotent stem cells (hiPS) has demonstrated a neuronal phenotype representing a powerful proof of concept of in vitro disease modeling, even for diseases with complex causation such as schizophrenia. These techniques have been used here to examine the behaviour of neural stem cells and neurons derived from fibroblasts from subjects carrying NDE1 copy number variations (CNVs) associated with increased risk of major mental illness. Using hiPS from individuals with and without disease-associated CNVs we have investigated how disease risk is conferred at a cellular and molecular level through detailed comparative studies of neural progenitor proliferation, neuronal morphology, physiology, cytoskeletal organization, synaptic function, glutamate (NMDA) receptor expression and also RNA sequencing and proteomic studies of these patient-derived cells.

| EGAS00001002895 | EGA

E-PROT-61

Project description:Proteomic Atlas of the Human Brain in Alzheimer's Disease

2021-05-25 | E-PROT-61 | ExpressionAtlas

E-PROT-31

Project description:Proteomic Atlas of the human brain in Alzheimer's disease

2021-05-25 | E-PROT-31 | ExpressionAtlas

Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics

Project description:The fatal neurodegenerative disorders amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) are the most common motoneuron disease and genetic cause of infant death, respectively. Various in vitro model systems have been established to investigate motoneuron disease mechanisms - in particular immortalized cell lines and primary neurons. By quantitative mass spectrometry (MS)-based proteomics we here compare the proteomes of primary motoneurons to motoneuron-like cell lines NSC-34 and N2a as well as to non-neuronal control cells at a depth of 10,000 proteins. We use this resource to evaluate the suitability of murine in vitro model systems for cell biological and biochemical analysis of motoneuron disease mechanisms. Individual protein and pathway analysis indicate substantial differences between motoneuron-like cell lines and primary motoneurons, especially for proteins involved in differentiation, cytoskeleton and receptor signaling, whereas common metabolic pathways were more similar. The ALS-associated proteins themselves also showed distinct differences between cell lines and primary motoneurons, providing a molecular basis for understanding fundamental alterations between cell lines and neurons with respect to neuronal pathways with relevance for disease mechanisms. Our study provides a proteomics resource for motoneuron research and presents a paradigm of how MS-based proteomics can be used to evaluate disease model systems

2020-02-08 | MSV000084939 | MassIVE

E-PROT-57

Project description:The Mount Sinai cohort of large-scale proteomic data in Alzheimer's disease

2021-05-20 | E-PROT-57 | ExpressionAtlas

Tlr7 mediates tissue-specific disease manifestations in primary Sjogren’s disease in a sex-biased manner

Project description:The goal of this study was to determine whether male and female mice with primary Sjogren's disease (pSD) displayed differences in autoreactive IgM and IgG in sera. We also sought to determine whether this reactivity was dependent on the expression of Tlr7.

2024-08-27 | GSE255215 | GEO

Striatal genes regulated by super-enhancers and displaying low paused RNAPII are preferentially down-regulated in Huntington’s disease [ChIP-seq]

Project description:Huntington neurodegenerative disease (HD) is associated with extensive down-regulation of neuronal genes. We show preferential down-regulation of super-enhancer-regulated neuronal function genes in the striatum of HD mice. Striatal super-enhancers display extensive H3K27 acetylation within gene bodies and drive transcription characterized by low levels of paused RNAPII. Down-regulation of gene expression is associated with diminished H3K27 acetylation and RNAPII recruitment. Striatal super-enhancers are enriched in binding motifs for Gata transcription factors, such as Gata2 regulating striatal identity genes. Thus, enhancer topography and transcription dynamics are major parameters determining the propensity of a gene to be deregulated in a neurodegenerative disease. Examination of H3k27ac and RNA pol II in Striatum by deep sequencing

2015-04-01 | E-GEOD-59570 | biostudies-arrayexpress

Fully defined NGN2 neuron protocol reveals diverse signatures of neuronal maturation

Project description:NGN2-driven iPSC-to-neuron conversion is a popular method for human neurological disease modeling. In this study, we report a fully standardized approach for generating functional excitatory cortical neurons. This method utilizes clonal, targeted-engineered iPSC lines and employs fully defined reagents. We demonstrate that our protocol generates consistent excitatory cortical neurons at scale. Comprehensive temporal omics, electrophysiological, and morphological profilings indicate the continued progression of neuronal maturation for at least 150 days. Deep quantitative characterizations through transcriptomic, imaging, and functional assays reveal coordinated actions of multiple pathways driving neuronal maturation. The neurons express the majority of the key risk genes in Alzheimer's disease, Parkinson's disease, and autism, demonstrating the relevance of our protocol in modeling human neurological disorders. This well-defined method, profiling data, and functional characterization provide a solid and reliable framework for developing human in vitro neuronal models for disease modeling.

2023-10-18 | MSV000093150 | MassIVE

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