Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolism of ethylene and epoxyethane by the methanotrophic bacterium Methylohalobius crimeensis

ABSTRACT: M. crimeensis contains an operon with a putative pathway for catabolic oxidation of epoxyethane to acetyl CoA. Proteomics was used to meausure the expression of the proteins encoded by this operon before and after ethylene exposure.

INSTRUMENT(S):

ORGANISM(S): Methylohalobius Crimeensis 10ki

SUBMITTER: Morgan Hepburn

LAB HEAD: Peter Dunfield

PROVIDER: PXD051614 | Pride | 2024-12-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MC_ethylene_MS2.mzML	Mzml
	MC_ethylene_MS2.raw	Raw
	checksum.txt	Txt
	peptide.tsv	Tabular
	protein.faa	Other

Items per page:

1 - 5 of 6

Similar Datasets

Accelerating Sample Preparation for Proteomics of Formalin Fixed Paraffin Embedded Tumor Tissues to Enable Biomarker Analysis

Project description:Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the crosslinking and pre-analytical variables, these samples have been demonstrated to be useful for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients’ medical histories. Proteomics of formalin fixed paraffin embedded (FFPE) tissues also integrates with histological and molecular pathology strategies, so that additional biopsies or resected tumor aliquots do not need to be used. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the sample preparation for FFPE can be onerous, particularly for very precious (i.e., limited) samples. Therefore, we compared a modified version of the well-established filter-aided sample preparation strategy to a recently introduced kit-based EasyPep method using laser capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables, while also enabling the development of methods for spatial proteomics to examine intratumoral heterogeneity.

2023-11-28 | PXD045879 | Pride

Interactome of the long non-protein coding RNA (lncRNA) D4Z4 binding element-transcript (DBE-T)

Project description:Facioscapulohumeral muscular dystrophy (FSHD) is an inherited progressive neuromuscular disorder that afflicts both children and adults regardless of gender. FSHD is caused by aberrant gain of expression of the transcription factor DUX4, which triggers a pro-apoptotic transcriptional program leading to muscle wasting. As today, no cure or therapeutic option is available to FSHD patients. Given its centrality in FSHD, blocking DUX4 expression with small molecule drugs is an attractive option. We previously showed that the long non-coding RNA DBE-T is required for aberrant DUX4 expression in FSHD. Using affinity purification followed by proteomics, we identified the chromatin remodeling protein WDR5 as a novel DBE-T interactor and a key player required for the biological activity of the lncRNA. We found that WDR5 is required for the expression of DUX4 and its targets in primary FSHD muscle cells. Moreover, targeting WDR5 rescues both cell viability and myogenic differentiation of FSHD patient cells. Notably, comparable results were obtained by pharmacological inhibition of WDR5. Importantly, WDR5 targeting was safe to healthy donor muscle cells. Our results support a pivotal role of WDR5 in the activation of DUX4 expression identifying a druggable target for an innovative therapeutic approach for FSHD.

2023-04-11 | PXD036038 | Pride

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress

Transcription profiling of rat at pheochromocytoma cell line PC12 treated with trimethyltin at low and high doses

Project description:The rat pheochromocytoma cell line PC12 cells were cultured in complete DMEM till 80% confluence, then placed at 5000 cells per squared cm. Cells were then plated in 24-well plates for cell viability assay and in T75 flasks for RNA isolation. Medium was replaced with serum-free fresh medium for 12 hours prior to TMT treatment. Gene expression patterns were then analysed using Rat Expression Array 230A Experiment Overall Design: In this study we analize gene expression patterns in PC12 cells treated with Trimethyltin (TMT). We utilized control cells (untreated) and two different concentration (1 and 5) Experiment Overall Design: We used three biological replicates, for the three concentration tested, according to MIAME guidelines Experiment Overall Design: (total 9 chips were used in this study).

2009-04-29 | E-GEOD-5073 | biostudies-arrayexpress

Shotgun proteome analysis of the bacterium Clostridium cellulolyticum

Project description:Biofuel production from lignocellulosic waste and residues is a promising option to mitigate the environmental costs associated to energy production. However, the difficulty to cost-effectively overcome lignocellulose recalcitrance hampers a widespread application of such bioprocesses. Through an integrated approach, we focused on the factors affecting cellulose reactivity and their impact on downstream fermentation. Three cellulosic manufactured materials were characterized in details: facial tissue, Whatman paper, cotton pads. The model mesophilic cellulolytic bacterium Clostridium cellulolyticum was used to study colonization and metabolic patterns during fermentation of these materials. Facial tissue was extensively colonized and exhibited the fastest degradation and the highest ethanol-to-acetate ratio. Comparing facial tissue fermentation to Whatman paper fermentation by label-free quantitative shotgun proteomics and statistical analyses, 187 proteins showed a different behavior; higher concentration levels were detected for many enzymes from the carbohydrate central metabolic pathway; distinct patterns of expression levels were observed for carbohydratases degrading cellulose and hemicellulose. Overall, lower degrees of polymerization, lower crystallinity index, and the presence of hemicelluloses could explain the higher biological reactivity and bioethanol production yields.

2017-01-30 | PXD001051 | Pride

Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation

Project description:E3 ubiquitin ligases are key enzymes within the ubiquitin proteasome system which catalyze the ubiquitination of proteins, targeting them for proteasomal degradation. E3 ligases are gaining importance as targets to small molecules, both for direct inhibition and to be hijacked to induce the degradation of non-native neo-substrates using bivalent compounds known as PROTACs (for ‘proteolysis-targeting chimeras’). We describe Homo-PROTACs as an approach to dimerize an E3 ligase to trigger its suicide-type chemical knockdown inside cells. We provide proof-of-concept of Homo-PROTACs using diverse molecules composed of two instances of a ligand for the von Hippel-Lindau (VHL) E3 ligase. The most active compound, CM11, dimerizes VHL with high avidity in vitro and induces potent, rapid and proteasome-dependent self-degradation of VHL in different cell lines, in a highly isoform-selective fashion and without triggering a hypoxic response. This approach offers a novel chemical probe for selective VHL knockdown, and demonstrates the potential for a new modality of chemical intervention on E3 ligases.

2018-10-24 | PXD007594 | Pride

Gene expression profiling of Eed knockout and Ezh2 knockout small intestinal crypts [ChIP-seq]

Project description:Polycomb-mediated gene repression plays an important role in adult stem cell maintenance. Direct targets of the Polycomb repressive complex PRC2 in th intestinal epithelium were revealed by performing ChIP-sequencing on crypt samples isolated from wild type murine small intestines. The resulting list of H3K27me3-enriched genes were compared with RNA-sequencing data from wild type and Eed knockout crypts. Crypts were isolated from wild type murine intestinal epithelium and subjected to ChIP using anti-H3K27me3 and anti-H3K27Ac antibodies, after which DNA isolated from extracted immunocomplexes was sequenced.

2016-07-01 | E-GEOD-81577 | biostudies-arrayexpress

Ethylene treated Arabidopsis roots

Project description:Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia) stress. The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced metabolic hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of primary Arabidopsis thaliana root tips.

2022-12-19 | PXD031138 | Pride

Evaluation and Optimization of High-Field Asymmetric Waveform Ion Mobility Spectrometry for Multiplexed Quantitative Site-specific N-glycoproteomics

Project description:The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative N-glycoproteomics have not been investigated yet. In this work, we optimized FAIMS settings for N-glycopeptide identification, with or without the tandem mass tag (TMT) label. The optimized FAIMS approach significantly increased the identification of site-specific N-glycopeptides derived from the purified IgM protein or human lymphoma cells. We explored in detail the changes in FAIMS mobility caused by N-glycopeptides with different characteristics, including TMT labeling, charge state, glycan type, peptide sequence, glycan size and precursor m/z. Importantly, FAIMS also improved multiplexed N-glycopeptide quantification, both with the standard MS2 acquisition method and with our recently developed Glyco-SPS-MS3 method. The combination of FAIMS and Glyco-SPS-MS3 provided the highest quantitative accuracy and precision. Our results demonstrate the advantages of FAIMS for improved mass-spectrometry-based qualitative and quantitative N-glycoproteomics.

2021-05-05 | PXD023951 | Pride

Microarray analysis of the effects of a Î³-tocopherol-rich mixture of tocopherols on global gene expression in the prostates of TRAMP mice

Project description:We used whole mouse genome microarrays to the effects of Î³-TmT on global gene expression in the prostate TRAMP and age-matched C57BL/6 mice were administered either 600 mg/kg of Î³-TmT or a control vehicle via oral gavage. Twelve hours after dosing, prostate tissues were collected for RNA extraction.

2014-09-16 | E-GEOD-61416 | biostudies-arrayexpress

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