Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time-series RNA-seq of U2OS cells following CCCP-induced mitochondrial damage and recovery upon drug washout

ABSTRACT: Mitochondria are continuously exposed to damage that contributes to aging and disease. While prolonged mitochondrial damage triggers mitophagy, how cells respond to transient damage remains unclear. To investigate the transcriptional programs underlying transient mitochondrial damage and subsequent recovery, we performed time-series RNA-seq analysis in human U2OS cells treated with the mitochondrial uncoupler CCCP. Four groups were analyzed: untreated control (WT), 50 μM CCCP for 30 min (CCCP), 50 μM CCCP for 30 min followed by 1 h washout (W1H), 50 μM CCCP for 30 min followed by 6 h washout (W6H). Each condition was analyzed in triplicate. This dataset reveals the dynamic transcriptional landscape during mitochondrial damage and recovery, highlighting the activation of stress-responsive transcription factors and antioxidant defense pathways that facilitate mitochondrial repair.

ORGANISM(S): Homo sapiens

PROVIDER: GSE342354 | GEO | 2026/08/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Time-series RNA-seq of U2OS cells following CCCP-induced mitochondrial damage and recovery upon drug washout

Project description:Time-series RNA-seq of U2OS cells following CCCP-induced mitochondrial damage and recovery upon drug washout

| PRJNA1507420 | ENA

Time-series of transcriptome analysis of Bacillus subtilis response to 25 mM potassium acetate and 0.85 M-BM-5M CCCP

Project description:The advent of M-bM-^@M-^XomicsM-bM-^@M-^Y techniques bear significant potential for the assessment of the microbiological stability of foods. This requires the integration of molecular data with their implication for cellular physiology. Here we performed a comparative physiological and transcriptional analysis of Bacillus subtilis stressed with three different weak organic acids: the commonly used food preservatives sorbic- and acetic- acid, plus the well-known uncoupler carbonyl cyanide-m-chlorophenyl hydrazone (CCCP). The concentration of each compound needed to cause a similar reduction of the growth rate negatively correlated with their membrane solubility, and positively with the concentration of undissociated acid. Intracellular acidification was demonstrated by expressing a pH-sensitive GFP derivative. The largest drop in intracellular pH was observed in CCCP-stressed cells and was accompanied by the transcriptional induction of the general stress response (GSR) and SigM regulon, responses known to be induced by acidification. The GSR was induced by acetate, but not by sorbate in mildly-stressed cells. Microarray analysis further revealed that all three acids activate transcriptional programs normally seen upon nutrient limitation and cause diverse responses indicative of an adaptation of the cell envelope. Based on the responses observed and the utilized pH measurements, the inhibitory effect of sorbic acid seems to be more focused on the cell membrane than that of acetic acid or CCCP. Time-series of B. subtilis response to 25 mM potassium acetate and 0.85 M-BM-5M CCCP during controlled growth in batch-fermentors in defined minimal medium (pH 6.4). Samples for microarrays were taken from both the treated and control cultures at 0, 10, 20, 30, 40, and 50 min after addition of acetate and CCCP. Two biologically independent experiments were performed.

2014-04-11 | E-GEOD-55051 | biostudies-arrayexpress

Quantitative chemical proteomics profile target proteins of ITCs

Project description:Quantitative chemical proteomics was performed to profile the target proteins of ITCs.For the forward SILAC experiment, heavy-labeled cells were treated with the ITC probe (20 μM) for 30 min and light-labeled cells were pre-treated with the natural ITC (60 μM) for 30 min, followed by the ITC probe (20 μM) for another 30 min. For the reverse SILAC experiment, light-labeled cells were treated with the ITC probe (20 μM) for 30 min and heavy-labeled cells were treated with the natural ITC (60 μM) for 30 min, followed by the ITC probe (20 μM) for another 30 min.

2025-05-06 | PXD051941 | Pride

Proteomic Profiling of Uveal Melanoma Cells Treated with DHA and CCCP

Project description:Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, with limited treatment options and poor clinical outcomes. Dihydroartemisinin (DHA), have shown anti-tumor activity in UM, though typically at high concentrations. This study investigates the synergistic anti-tumor effects of combining DHA with a mitochondrial uncoupler CCCP. We treated UM cells with DHA and/or CCCP, and then proteomic profiling was performed to elucidate molecular mechanisms underlying the enhanced efficacy of the combination treatment. Our results indicate that co-treatment induces endoplasmic reticulum stress and activates autophagic cell death pathways, highlighting a potential combinatorial therapeutic strategy for UM.

2025-06-10 | PXD064150 | Pride

Analysis of neuronal phosphoproteome reveals PINK1 regulation of BAD function and cell death

Project description:We interrogated whether there existed a broader effect of PINK1-dependent phosphorylation after mitochondrial damage by utilizing primary cultured neurons from WT and Pink1 KO mice. Because persistent depolarization leads to mitochondrial damage {}, we treated cultured neurons with the protonophore carbonyl cyanide m-chlorophenyl hydrazine (CCCP) and blotted for PINK1. Consistent with previous studies, CCCP treatment results in an upregulation of endogenous PINK1 in WT neurons. Endogenous PINK1 is undetectable in Pink1 KO neurons with CCCP treatment.Overall, our phosphoproteome analysis of biological duplicates experiments quantified 10930 and 7207 phosphorylation sites, respectively, from the early (designated as 15-45 min) and late (designated as 2-6 hr) treatment time points

2017-04-14 | MSV000080923 | MassIVE

Transcriptome analysis after CCCP and/or DHA treatment in uveal melanoma cells

Project description:In order to study the mechanism of CCCP combined with DHA treatment in uveal melanoma, we applied RNA-seq to identify its target genes in ocular melanoma.

2024-06-01 | GSE176474 | GEO

Alterations in the nascent proteome during translation attenuation in response to mitochondrial stress induced by carbonyl cyanide m-chlorophenyl hydrazine (CCCP) and in response to EEF1A1 knockdown

Project description:This submission is a part of a proteomic resource consisting of four independent datasets and their meta-analysis which describe: the detailed landscape of changes in the nascent proteome at high temporal resolution with 30 min intervals upon rapid and reversible global translation attenuation in response to transient mitochondrial membrane depolarization and during the subsequent recovery of physiological translation upon the relief of this stress (PXD043942), comparison of nascent proteome alterations in response to two types of challenge to protein homeostasis – proteasome inhibition and mitochondrial inner membrane depolarization (this submission, datasets expII and expIV) and finally nascent proteome alterations happening after silencing of elongation factor EEF1A1 in untreated and stress conditions (this submission, dataset expIII).

2024-10-02 | PXD054502 | Pride

Genome-wide Transcriptional Profiling of Bacillus subtilis in response to valinomycin and CCCP

Project description:Valinomycin is a cyclic depsipeptide antibiotic produced by Streptomyces fulvissimus, and also known as K+ ion-selective ionophore, that has been studied and used in research for over half of century. The broad antimicrobial activity of valinomycin is reported as an effect of the disturbance of ionic equilibrium and transmembrane potential that may influence the whole organism and then cause fatal consequences. CCCP, carbonyl cyanide 3-chlorophenylhydrazone, is a member of the lipophilic weak acid class and acts essentially as an ionophore and can reduce the overall metabolic activity of the cell, causing severe defects of cell growth. In this study, we investigated the global cellular response of Gram-positive model bacterium Bacillus subtilis upon exposure to valinomycin as well as CCCP by genome-wide transcriptional profiling using RNA sequencing technique, aimed to unveil the underlying regulatory network of the stress response.

2025-10-28 | GSE160346 | GEO

Analysis of phosphoproteome reveals PINK1 regulation of BAD function and cell death

Project description:We interrogated whether there existed a broader effect of PINK1-dependent phosphorylation after mitochondrial damage by utilizing primary cultured neurons from WT and Pink1 KO mice. Because persistent depolarization leads to mitochondrial damage, we treated cultured neurons with the protonophore carbonyl cyanide m-chlorophenyl hydrazine (CCCP) and blotted for PINK1. Overall, our phosphoproteome analysis of biological duplicates experiments quantified 10930 and 7207 phosphorylation sites, respectively, from the early (designated as 15-45 min) and late (designated as 2-6 hr) treatment time points.

2017-04-08 | MSV000080893 | MassIVE

Shewanella oneidensis outer membrane and outer membrane vesicles

Project description:This project compares the outer membrane proteome to the proteome of outer membrane vesicles of the bacterium Shewanella onedensis. S. oneidensis outer membrane was purified via the sarkosyl method described in (Brown, 2010). A 50 mL overnight culture of cells were harvested by centrifugation at 10,000× g for 10 min. cell pellet suspended in 20 mL of 20 mM ice-cold sodium phosphate (pH 7.5) and passed four times through a French Press (12000 lb/in2). The lysate was centrifuged at 5,000× g for 30 min to remove unbroken cells. The remaining supernatant was centrifuged at 45,000 × g for 1 h to pellet membranes. Crude membranes were suspended in 20 mL 0.5% Sarkosyl in 20 mM sodium phosphate and shaken horizontally at 200 rpm for 30 min at room temperature. The crude membrane sample was centrifuged at 45,000 × g for 1 h to pellet the OM. The pellet of OM was washed in ice-cold sodium phosphate and recentrifuged. The cells were pelleted by centrifugation at 5000 x g for 20 min at 4°C, and the supernatant was filtered through 0.45 μm pore size filters to remove remaining bacterial cells. Vesicles were obtained by centrifugation at 38,400 x g for 1 h at 4°C in an Avanti J-20XP centrifuge (Beckman Coulter, Inc). Pelleted vesicles were resuspended in 25 ml of 50 mM HEPES (pH 6.8) and filtered through 0.45 μm pore size filters. Vesicles were again pelleted as described above and finally resuspended in 50 mM HEPES, pH 6.8. Extracellular DNA, flagella, and pili can all be co-purified. Protocol was adapted from (Perez-Cruz, 2013).

2021-11-10 | PXD020577 | Pride

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