Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subcellular proteomics of murine ESC-derived neurons

ABSTRACT: We studied the effects of different stimuli on on the subcellular proteome of neurons differentiated from murine embryonic stem cells (ESC). We focused on the changes in the chromatin-bound fraction to elucidate specific differences in the gene regulatory machinery activated upon stimulation with Brain-derived neurotrophic factor (BDNF) or a general membrane-depolarization stimulus, potassium chloride (KCl).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Neuron, Cell Culture

SUBMITTER: Henrik Hammarén

LAB HEAD: Mikhail M Savitski

PROVIDER: PXD022378 | Pride | 2022-09-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements.

Ibarra Ignacio L IL Ratnu Vikram S VS Gordillo Lucia L Hwang In-Young IY Mariani Luca L Weinand Kathryn K Hammarén Henrik M HM Heck Jennifer J Bulyk Martha L ML Savitski Mikhail M MM Zaugg Judith B JB Noh Kyung-Min KM

Molecular systems biology 20220801 8

Neuronal stimulation induced by the brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin ...[more]

PMID: 35996956

Similar Datasets

Subcellular proteomics of murine presomitic mesoderm

Project description:We studied the effects of different stimuli on on the subcellular proteome of primary murine presomitic mesoderm tissue (PSM) in two separate experiments. In the first experiment, tissue was treated ex vivo with either fructose-6-phosphate, fructose-1,6-bisphosphate, or control treatment before subcellular fractionation using a subcellular protein fractionation kit (Thermo Fisher Scientific 78840). In the second experiment, PSMs from transgenic and control mice were extracted and subcellularly fractionated as above. Samples were multiplexed using TMT and analyzed on LC-MS/MS.

2022-12-07 | PXD029988 | Pride

PhosphoProtein-Peptide Turnover Profiling, validation

Project description:We combined pulsed stable isotope labeling of amino acids (pSILAC) with enrichment of phosphorylated peptides in a method we term PhosphoProtein-Peptide Turnover Profiling (PhosphoPPToP). We applied the method to HeLa cells to find peptides whose clearance rates differ from the protein median. Using theoretical modelling, we show that readouts from PPToP are primarily defined by the wiring of the PTM-modification network and not by effects of the PTM on a protein's proteolytic stability. Thus PPToP can be used to identify PTMs occurring, e.g., preferentially early or late in a protein's lifetime. This enables identification of, e.g., protein maturation or protein complex assembly intermediates. This dataset covers experimental testing of identified phosphosites with PPToP. Here, proteins of interest are expressed as GFP-fusion constructs in HeLa cells and subjected to a SILAC pulse. Thereafter, proteins are pulled-down with anti-GFP beads to isolate the exogenously expressed constructs. We multiplex SILAC timepoints from wild-type and mutant constructs for every given protein of interest using TMT16.

2022-12-02 | PXD032945 | Pride

Delineation of the pH-responsive regulon controlled by the Helicobacter pylori ArsRS two2 component system

Project description:Helicobacter pylori encounters a wide range of pH within the human stomach. In a comparison of H. pylori cultured in vitro under neutral or acidic conditions, about 15% of genes are26 differentially expressed, and corresponding changes are detectable for many of the encoded proteins. The ArsRS two-component system (TCS), comprised of the sensor kinase ArsS and its cognate response regulator ArsR, has an important role in mediating pH-responsive changes in H. pylori gene expression. In this study, we sought to delineate the pH-responsive ArsRS regulon and further define the role of ArsR in pH-responsive gene expression. We compared H. pylori strains containing an intact ArsRS system with an arsS null mutant or strains containing site32 specific mutations of a conserved aspartate residue (D52) in ArsR, which is phosphorylated in response to signals relayed by the cognate sensor kinase ArsS. We identified 178 genes that were pH-responsive in strains containing an intact ArsRS system but not in ∆arsS or arsR mutants. These constituents of the pH-responsive ArsRS regulon include genes involved in acid acclimatization (ureAB, amidases), oxidative stress responses (katA, sodB), transcriptional regulation related to iron or nickel homeostasis (fur, nikR), and genes encoding outer membrane proteins [including sabA, alpA, alpB, hopD (labA), and horA]. When comparing H. pylori strains containing an intact ArsRS TCS with arsRS mutants, each cultured at neutral pH, relatively few genes are differentially expressed. Collectively, these data suggest that ArsRS41 mediated gene regulation has an important role in H. pylori adaptation to changing pH conditions.

2022-02-16 | PXD023679 | Pride

Complexome Profiling of the mitochondrial proteome from Viscum album

Project description:Viscum album is known for its special mode of cellular respiration. It lacks the mitochondrial NADH dehydrogenase complex (complex I of the respiratory chain) and has restricted capacities to generate mitochondrial adenosine triphosphate (ATP). We here present an investigation of the V. album energy metabolism taking place in mitochondria. Mitochondria were purified from young V. album leaves and membrane bound protein complexes characterized by Blue native polyacrylamide gel electrophoresis as well as by the complexome profiling approach. Proteins were systematically identified by label-free quantitative shotgun proteomics.

2023-10-24 | PXD041061 | Pride

Proteomic analysis of primary human microvascular endothelial cells (HMVECs) stimulated for 24â€‰h with either 50 ï�g/mL recombinant Fibrillin-1 C-terminal fragment or 25â€‰ng/ml VEGF-A compared to unstimulated cells.

Project description:Mutations in the fibrillin-1 gene result in cardiovascular, ocular, and skeletal abnormalities in Marfan syndrome. Here we show that a fibrillin-1 mutation also alters the neovessel formation. In the mouse retina vascularization model, fibrillin-1 is detected at the basement membrane underlying the angiogenic front and around arterioles. In Fbn1C1041G/+ mice, a model of Marfan disease, the microvasculature is altered at these sites. At the front, endothelial tip-cell sprouting and branching are decreased, and we show that mutant fibrillin-1 delays angiogenesis by affecting Notch signalling. Supplying the growing vasculature of Fbn1C1041G/+ mice with a C-terminal fragment of fibrillin-1 corrects all defects. In vitro, the C-terminal fragment of fibrillin-1 also displays pro-angiogenic activities on microvascular endothelial cell. Our data establish that fibrillin-1 performs essential functions in microvessel formation and integrity and that mutant fibrillin-1-induced defects can be rescued pharmacologically.

2023-05-31 | PXD029834 | Pride

PhosphoProtein-Peptide Turnover Profiling, exploratory

Project description:We combine pulsed stable isotope labeling of amino acids (pSILAC) with enrichment of phosphorylated peptides in a method we term PhosphoProtein-Peptide Turnover Profiling (PhosphoPPToP). We apply the method to HeLa cells to find peptides whose clearance rates differ from the protein median. Using theoretical modelling, we show that readouts from PPToP are primarily defined by the wiring of the PTM-modification network and not by effects of the PTM on a protein's proteolytic stability. Thus PPToP can be used to identify PTMs occurring, e.g., preferentially early or late in a protein's lifetime. This enables identification of, e.g., protein maturation or protein complex assembly intermediates.

2022-12-02 | PXD033254 | Pride

BioID with P. falciparum protein PhiL1

Project description:The aim of the project was to identify proteins proximal to Plasmodium falciparum PhiL1

2021-05-03 | PXD024237 | Pride

Regulating hippocampal levels of AlzheimerÃ‚Â´s disease-related proteins with a brain-penetrating somatostatin peptide

Project description:Plaques consisting of amyloid-ÃŽÂ² (AÃŽÂ²) in the brain are characteristic for patients with AlzheimerÃ‚Â´s disease. AÃŽÂ² is enzymatically generated of the amyloid precursor protein. Furthermore, neprilysin, an AÃŽÂ²-degrading enzyme, and its main activator the neuropeptide somatostatin (SST) are downregulated in AlzheimerÃ‚Â´s disease. In the fusion protein SST-scFv8D3, SST is recombinantly fused to a blood-brain barrier transporter. The aim of this study was to study the effect of SST-scFv8D3 on the proteome of different brain regions in order to elucidate the anti-AlzheimerÃ‚Â´s disease effects of this construct. SST-scFv8D3 and phosphate buffered saline (PBS) respectively were injected into transgenic mice of an AlzheimerÃ‚Â´s disease model with the Swedish mutation (AÃŽÂ²PP KM670/671NL) every 36 hours (three times in total). Homogenates of the hippocampus, the cerebellum and the rest of the cerebrum were lysed. Afterwards, filter aided tryptic digestion was performed. The resulting peptides were analyzed using LC-UDMSE. The data was searched against a randomized mouse database and label-free quantification analysis was done. In total 1869 proteins were found. Only the proteome of the hippocampus was affected by the treatment with SST-scFv8D3. 55 proteins were significantly up and 105 down regulated compared to the PBS treated mice. Among these were mitochondrial and synaptic proteins as well as some involved in neuronÃ‚Â´s development indicating anti-Alzheimer disease effects of SST-scFv8D3 and supporting the future use of SST-scFv8D3 as a treatment option.

2021-06-28 | PXD022221 | Pride

Enhanced RNA interactome capture (eRIC) of human malignant bone tumor cells and normal bone/mesenchymal cells

Project description:Patient-derived bone tumor (osteosarcoma and giant cell tumor of bone) cells, and the normal mesenchymal stem cells and osteoblasts were cultured and subjected to UV crosslinking (UV) at 254 nm or without crosslinking (noUV) as negative controls. Subsequently, RNA-binding proteins (RBPs) were identified by eRIC.

2024-02-28 | PXD038185 | Pride

Aspartoacylase-dependent transcriptome changes in immortalized brown adipocytes

Project description:Here we investigated the effect of stable knock-down of the NAA-catabolizing enzyme, Aspartoacylase (Aspa), on global gene expression in a brown adipocyte cell line. Immortalized brown adipogenic cells (iBACs) with stable Aspa knock-down and control cells were grown until confluence and then differentiated. Cells were harvested on day 7. Experiment was done in triplicates with three different passages.

2016-02-29 | E-GEOD-65906 | biostudies-arrayexpress

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