Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nitroxoline Resistance in Escherichia coli

ABSTRACT: Profiling of Nitroxoline resistance in Escherichia coli using full proteome analysis

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Escherichia Coli

SUBMITTER: Felix Deschner

LAB HEAD: Rolf Mueller

PROVIDER: PXD046609 | Pride | 2023-11-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Analyses of Rad2, Mediator and RNA Polymerase II in different yeast mutant context.

Project description:We performed ChIP-seq analyses of Rad2, Mediator (Med17 and Med5) and RNA Polymerase II in Kin28-ts16 mutant, Med17-Q444P and Med17-Q444P/M442L mutants and in an Rpb9 deleted strain.

2019-07-01 | E-MTAB-7081 | biostudies-arrayexpress

ClariomS Array to determine the impact of whole body adenylyl cyclase 5 (Adcy5) knockout on male/female epigonadal white adipos tissue (eWAT) gene expression

Project description:We analyzed the effect of whole body Adcy5 knockout on adipose tissue gene expression profiles. Therefore, we isolated RNA, examined RNA integrity and concentration on an Agilent Fragment Analyzer using the HS RNA Kit. cRNA was prepared from 100 ng of total RNA hybridized to GeneChip Clariom S arrays. The arrays were scanned with a third generation Affymetrix GeneChip Scanner 3000.

2021-04-19 | E-MTAB-9417 | biostudies-arrayexpress

Rapid and ion mobility-resolved phosphoproteomics with dia-PASEF

Project description:Mass spectrometry-based phosphoproteomics has identified >150,000 post-translational phosphorylation sites in the human proteome. To disentangle their functional relevance, complex experimental designs that require increased throughput are now coming into focus. Here, we apply dia-PASEF on a trapped ion mobility (TIMS) mass spectrometer to analyze the phosphoproteome of a human cancer cell line in short liquid chromatography gradients. At low sample amounts equivalent to ~20 ug protein digest per analysis, we quantified over 13,000 phosphopeptides including ~8,700 class I phosphosites in one hour without a spectral library. Decreasing the gradient time to 15 min yielded virtually identical coverage of the phosphoproteome, and with 7 min gradients we still quantified about 80% of the class I sites with a median coefficient of variation <10% in quadruplicates. We attribute this in part to the increased peak capacity, which effectively compensates for the higher peptide density per time unit in shorter gradients. Our data shows a five-fold reduction in the number of co-isolated peptides with TIMS. In the most extreme case, these were positional isomers of nearby phosphosites that remained unresolved with fast chromatography. In summary, our study demonstrates how key features of dia-PASEF translate to phosphoproteomics.

2022-10-26 | PXD033904 | Pride

Rpc160-TAP ChIP-chip from S. cerevisiae

Project description:ChIP-chip was performed to identify RPC160 binding locations in S. cerevisiae

2015-07-08 | E-MTAB-3700 | biostudies-arrayexpress

Comparative genomic hybridization of 17 strains of Ralstonia solanacearum, one strain of R. syzygii and one strain of R. pickettii

Project description:comparison of gene content between 17 strains of Ralstonia solanacearum, one strain of R. syzygii and one strain of R. pickettii

2006-11-25 | E-MEXP-851 | biostudies-arrayexpress

Mitoribosome profiling (MitoRiboSeq) data from HEK WT and mtRF1 knockout cell lines

Project description:Mitochondrial translation was investigated by mitochondrial ribosome profiling (mitoRiboSeq) in three HEK293 cell lines: HEK293 wildtype, mtRF1 knockout 1, and mtRF1 knockout 2

2022-12-01 | E-MTAB-11687 | biostudies-arrayexpress

Vagus Nerve Stimulation enhances remyelination and decreases innate neuroinflammation in a Multiple Sclerosis rodent model.

Project description:This study investigated the effect of Vagus Nerve Stimulation (VNS) on innate neuroinflammation and remyelination in lysolecithin (LPC) induced demyelination, a preclinical model for Multiple Sclerosis (MS). In a first experiment (demyelination experiment), LPC was injected in the corpus callosum of 33 Lewis rats, inducing a demyelinated lesion, and rats were treated with either continuously-cycled VNS (cVNS) or one-minute per day VNS (1minVNS) or sham VNS, from two days before the injection until three days post-injection (dpi), when they were killed for immunohistochemistry and proteomics analysis. This timepoint corresponded with a demyelinated lesion and peak inflammation. In a second experiment (remyelination experiment), 13 rats were analogously treated with either cVNS or sham from two days before LPC injection until 11 dpi, when they were killed for tissue prelevation for immunohistochemistry and proteomics. This timepoints corresponded with partial remyelination of the lesion. For proteomics analysis, 20 rats were randomly selected, namely five cVNS and five sham rats of the demyelination experiment, and five cVNS and five sham rats of the remyelination experiment.

2024-05-10 | PXD050858 | Pride

Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

Project description:The poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptomewide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale coexpression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. Analysing long and short poly(A)-tail fractions from 4 paps1 mutant and 4 Ler samples.

2015-07-30 | E-GEOD-57690 | biostudies-arrayexpress

A chemical probe to monitor parkinsonism-associated protein DJ-1 in live cells

Project description:Oxidative stress is a contingent trigger of Parkinson`s disease (PD). DJ-1, a protein involved in oxidative stress sensing, gained major attention when mutations in its gene were identified in PD patients. Although the study of the corresponding protein function is still in its infancy, a crucial oxidation sensor at a conserved cysteine was linked to the disease. Inspired by inhibition studies with a bacterial homolog of DJ-1 we here screen several amino-epoxycylcohexenones and identify a chemical probe that exhibits specificity for the human protein in various cell lines. The probe selectively labeled the oxidation sensor via nucleophilic attack of the conserved cysteine onto the epoxide ring. This covalent addition occurred only in the reduced state. Whole proteome studies in HeLa, A549 and SHSY5Y cell lines confirmed strong enrichment of solely reduced DJ-1 which was diminished by increasing oxidative stress. The probe thus facilitates the first selective in situ monitoring of DJ-1 in its reduced state and enables studying the function of this important biomarker in dependence of oxidative stress.

2018-07-17 | PXD009444 | Pride

Tranylcypromine specificity for monoamine oxidase is limited by promiscuous protein labelling and lysosomal trapping

Project description:Monoamine oxidases MAOA and MAOB catalyze important cellular functions such as the deamination of neurotransmitters. Correspondingly, MAO inhibitors are used for the treatment of severe neuropsychiatric disorders such as depression. A commonly prescribed drug against refractory depression is tranylcypromine, however, the side effects are poorly understood. In order to decipher putative off-targets, we synthesized two tranylcypromine probes equipped with either an alkyne moiety or an alkyne-diazirine minimal photocrosslinker for in situ proteome profiling. Surprisingly, LC-MS/MS analysis revealed low enrichment of MAOA and relatively promiscuous labeling of proteins. Photoprobe labeling paired with fluorescent imaging studies revealed lysosomal trapping which could be largely reverted by the addition of lysosomotropic drugs.

2020-10-20 | PXD018580 | Pride

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