Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of PHIKZ-infected PAO1 cells after ASO KD of chmA, nvRNAP, picA

ABSTRACT: Proteomics of PHIKZ-infected cells after ASO-based knockdown. We show specific knockdown of targeted proteins with limited off-targets.

INSTRUMENT(S):

ORGANISM(S): Pseudomonas Aeruginosa Pao1h2o Bacteria

SUBMITTER: Milan Gerovac

LAB HEAD: Jörg Vogel

PROVIDER: PXD062538 | Pride | 2025-07-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Ernie_240207_P3700_JS_MG_125_10min_2of20_R1.raw	Raw
	Ernie_240207_P3700_JS_MG_125_2p5min_2of20_R1.raw	Raw
	Ernie_240207_P3700_JS_MG_125_5min_2of20_R1.raw	Raw
	Ernie_240207_P3700_JS_MG_125_7p5min_2of20_R1.raw	Raw
	Ernie_240207_P3700_JS_MG_72_10min_2of20_R1.raw	Raw

Items per page:

1 - 5 of 22

Similar Datasets

Grad-MS PHIKZ phage infected Pseudomonas aeruginosa PAO1 cells

Project description:Protein complexes in phage infected cells probed by MS.

2024-02-03 | PXD038771 | Pride

NAD capping of mRNAs is abundant but strongly guarded against in yeast

Project description:The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5'-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG motif for this purpose. Most NAD-RNAs are 3'-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

2020-09-02 | PXD017893 | Pride

BioID with P. falciparum protein SPM3

Project description:The aim of the project was to identify proteins proximal to Plasmodium falciparum SPM3

2025-12-02 | PXD060994 | Pride

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation

Project description:A progressive loss of protein homeostasis is characteristic of aging and a driver of neurodegeneration. To investigate this process quantitatively, we characterized proteome dynamics during brain aging in the short-lived vertebrate Nothobranchius furzeri combining transcriptomics and proteomics. We detected a progressive reduction in the correlation between protein and mRNA mainly due to post-transcriptional mechanisms that account for over 40% of the age-regulated proteins. These changes cause a progressive loss of stoichiometry in several protein complexes, including ribosomes, which show impaired assembly and are enriched in protein aggregates in old brains. Mechanistically, we show that reduction of proteasome activity is an early event during brain aging and is sufficient to induce proteomic signatures of aging and loss of stoichiometry in vivo. Using longitudinal transcriptomic data, we show that the magnitude of early life decline in proteasome levels is the major risk factor for mortality. Our work defines causative events in the aging process that can be targeted to prevent loss of protein homeostasis and delay the onset of age-related neurodegeneration.

2020-06-22 | PXD016587 | Pride

Nutlin-3a-induced changes in the proteome of parental and RFX7 knock-out U2OS cells

Project description:Mass spectrometry-based whole proteome analysis of parental and RFX7 knock-out U2OS cells treated with 10 µM Nutlin-3a or DMSO solvent control. Ten biological replicates were used.

2023-03-11 | PXD024869 | Pride

Crosslinking-MS dataset of the TFIIIC subcomplex tauA with Brf1 and TBP

Project description:Identification of crosslinks between the subunits tau131, tau95, tau55, Brf1 and TBP

2020-12-04 | PXD018232 | Pride

Impact of mannosylation on structure and functionality of ER and Golgi

Project description:Many proteins undergo glycosylation in the endoplasmic reticulum (ER) and the Golgi apparatus. Altered glycosylation can manifest in serious, sometimes fatal malfunctions. We recently showed that mutations in the cytoplasmic protein GDP-mannose pyrophosphorylase A (GMPPA) cause a syndrome characterized by alacrima, achalasia, mental retardation and myopathic alterations. GMPPA acts as feedback inhibitor of GDP-mannose pyrophosphorylase B (GMPPB), which provides GDP-mannose as a substrate for protein glycosylation. Loss of GMPPA enhances incorporation of mannose into glycochains of various proteins, including α-dystroglycan (α-DG), a protein that links the extracellular matrix with the cytoskeleton. Here, we show that loss of GMPPA affects the functionality of the Golgi apparatus using different approaches. First, we show a fragmentation of the Golgi apparatus in skeletal muscle fibers and in neurons of GMPPA KO mice. A major reorganization is also evident by mass spectrometry of KO tissues with a regulation of several ER- and Golgi-resident proteins. We further show that loss of GMPPA increases the retention of α-DG in the ER. Notably, mannose supplementation can mimic changes in ER and Golgi structure and function in WT cells. In summary, our data underline the importance of a balanced mannose homeostasis for structure and function of the secretory pathway.

2023-03-11 | PXD037129 | Pride

Enhanced feature matching in single-cell proteomics characterizes response to IFN-γ and reveals co-existence of different cell states-Bulk Proteomics experiment

Project description:Proteome analysis by data-independent acquisition (DIA) has become a powerful approach to obtain deep proteome coverage, and has gained recent traction for label-free analysis of single cells. However, optimal experimental design for DIA-based single-cell proteomics has not been fully explored, and performance metrics of subsequent data analysis tools remain to be evaluated. Therefore, we here present DIA-ME, a data analysis strategy that exploits the co-analysis of low-input samples with a so-called matching enhancer (ME) of higher input, to increase sensitivity, proteome coverage, and data completeness. We evaluate the matching specificity of DIA-ME by a two-proteome model, and demonstrate that false discovery and false transfers are maintained at low levels when using DIA-NN software, while preserving quantification accuracy. We apply DIA-ME to investigate the proteome response of U-2 OS cells to interferon gamma (IFN-γ) in single cells, and recapitulate the time-resolved induction of IFN-γ response proteins as observed in bulk material. Moreover, we observe co- and anti-correlating patterns of protein expression within the same cell, indicating mutually exclusive protein modules and the co-existence of different cell states. Collectively our data show that DIA-ME is a powerful, scalable, and easy-to-implement strategy for single-cell proteomics.

2024-08-22 | PXD048162 | Pride

Specialized replication mechanisms maintain genome stability at human centromeres

Project description:Reveal a specific set of proteins important to maintain centromere integrity, through quantitative PICh (Proteomics of Isolated Chromatin). Centromeric chromatin was pulled down through RNA probes annealing specifically to a 300bp-long conserved centromeric sequence.

2024-02-14 | PXD047847 | Pride

Integrated phosphoproteome, ubiquitinome, and acetylome analyses uncovering the post-translational modifications crosstalk during MSP1-induced signaling in rice

Project description:Magnaporthe oryzae snodprot1 homologous protein (MSP1) has been shown to act as a pathogen-associated molecular pattern (PAMPs) and trigger PAMP-triggered immunity (PTI) response involving programmed cell death and expression of various defense-related genes in rice. The involvement of several post-translational modifications (PTMs) in the regulation of plant immune response, especially PTI, during pathogen infection is well established, however, the information on the regulatory roles of these PTMs in response to MSP1-induced signaling in rice is currently elusive. Here, we report the phosphoproteome, ubiquitinome, and acetylproteome to investigate the MSP1-induced PTMs alterations in MSP1 overexpressed rice. Our analysis identified a total of 4,666 PTM modified sites in rice leaves including 4,292 phosphosites, 189 ubiquitin sites, and 185 acetylation sites. Among these, PTM status of 437 phosphorylated, 53 ubiquitinated, and 68 acetylated peptides were significantly changed by MSP1. Functional annotation of MSP1 modulated peptides by MapMan analysis revealed that these were majorly associated with cellular immune responses such as signaling, transcription factors, DNA and RNA regulation, and protein metabolism, among others. Taken together, this study uncovers the MSP1-induced PTMs changes in rice proteins and identified several novel components of rice-MSP1 interaction.

2023-07-21 | PXD039997 | 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