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ProteomicsQuantitative phosphoproteomics to unravel the cellular response to chemical stressors with different modes of action
Cells activate various stress response pathways when exposed to chemicals that can damage cellular macromolecules and organelles. Whether different chemical stressors activate common and/or stressor-specific pathways and to what extent is largely unclear. Here, we used quantitative phosphoproteomics...
ORGANISM(S): Mus musculus (Mouse) 
2020-03-23 | PXD012559 | Pride
Phosphoproteomics Topbp1 Mdc1 Post-translational modification Mass spectrometry Cyclosporinea Mouse Biological Phosphorylation Lc-msms Mescs Atr Atm Silac Signal transduction Diethylmaleate Etoposide Cisplatin Rad51 
ProteomicsPhosphoproteomics sample preparation impacts biological interpretation of signalling responses
Quantitative data-dependent acquisition phosphoproteomics (DDAP) has revolutionised cell signaling studies. However, the impact of the specific DDAP sample preparation method on the phosphoproteome quantified is unclear as each study quantifies only a fraction of the phosphoproteome. Here, we compar...
ORGANISM(S): Mus musculus (Mouse) 
2021-12-25 | PXD025376 | Pride
Phosphoproteomics Tio2 Mouse High-throughput phosphoproteomics Scxphos Sample preparation Highphos Comparative analysis 
ProteomicsMouse ESC LC-MSMS Ionising radiation
Dose-dependent (phospho) proteome responses of mouse embyronic stem cells to ionising radiation. Quantitative SILAC- and mass spectrometry-based proteomics and phosphoproteomics experiments were performe at half an hour (0.5h) and four hours (4h) after exposure to LD (0.1 Gy) and high doses (HD; 1 G...
ORGANISM(S): Mus musculus (Mouse) 
2022-03-18 | PXD025343 | Pride
Reactive oxygen species Transporter Phosphoproteome Ionising radiation Mouse Mitochondria Proteome Dna damage response 
TranscriptomicsTranscription profiling of rat cardiac myocytes and fibroblasts subjected to 24 hours of mechanical stress, or treated with a single dose of ionizing or ultraviolet radiation and allowed to recover for 24 hours
Rationale: During excessive pressure or overload, cardiac cells are subjected to increased mechanical stress. We investigate how the stress response of cardiac cells to mechanical stress can be compared to genotoxic stresses induced by DNA damaging agents. Methods: Cultures enriched for cardiomyocyt...
ORGANISM(S): Rattus norvegicus 
2007-09-18 | E-GEOD-2032 | biostudies-arrayexpress
ProteomicsThe dynamics of Atm signalling dictate cellular fate decisions after DNA damage
DNA damage activates diverse cellular responses – either protective or deleterious –that ultimately promote or inhibit proliferation. How the distinct responses conferring crucial cell fate decisions are chosen is unclear. Using a systems approach, we demonstrate that the dynamic features of Atm...
ORGANISM(S): Mus musculus (Mouse) 
2023-01-18 | PXD013620 | Pride
Phosphoproteomics Mdc1 Post-translational modification Mass spectrometry Mouse Ionizing radiation Biological Phosphorylation Lc-msms Mescs Atm Silac Signal transduction Chek2 
TranscriptomicsTranscription profiling of irradiated human lymphocytes from prostate carcinoma patients following curative radiotherapy to study late radiation toxicity
For a case-control study, we selected 54 prostate carcinoma patients with no evidence of disease 2 years after curative
ORGANISM(S): Homo sapiens 
2007-12-01 | E-TABM-90 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse embryonic stem cells exposed to cisplatin at four time points and concentrations to investigate DNA damage signalling pathways
To gain insight in the kinetics and interplay of the predominant transcriptional responses of DNA damage signalling pathways in undifferentiated cells, mouse embryonic stem cells were exposed to cisplatin at four different time points (2, 4, 8 and 24 hr) and concentrations (1, 2, 5 and 10 uM). RNA w...
ORGANISM(S): Mus musculus 
2006-04-27 | E-TABM-89 | biostudies-arrayexpress
TranscriptomicsDeciphering the RNA landscape by RNAome sequencing [Seq]
Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single...
ORGANISM(S): Mus musculus 
2015-04-01 | E-GEOD-48083 | biostudies-arrayexpress
Genomicsena-DATASET-UMCU-10-10-2018-09:56:24:582-1061 - samples
WGS of ovarian cancer organoids, tumor samples and blood references. Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a nove...
EGAD00001004387 | EGA
Genomicsena-DATASET-UMCU-04-11-2019-12:52:17:220-46 - samples
WGS Nanopore nanopore sequencing of organoid line HGS-3.1 and matching blood reference HGS-3
EGAD00001005476 | EGA
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