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TranscriptomicsThe stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression
The stringent response is initiated by rapid (p)ppGpp synthesis, which leads to a profound reprogramming of gene expression in most bacteria. The stringent phenotype seems to be species specific and may be mediated by fundamentally different molecular mechanisms. In Staphylococcus aureus, (p)ppGpp s...
ORGANISM(S): Staphylococcus aureus 
2013-04-05 | E-GEOD-45617 | biostudies-arrayexpress
ProteomicsDDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics
This project provides a large-scale training dataset for DDA-BERT, an end-to-end transformer-based deep learning model developed for PSM rescoring in data-dependent acquisition (DDA) proteomics. The dataset comprises curated PSMs generated using established database search engines, including FragPip...
ORGANISM(S): Chlamydomonas reinhardtii Glycine max Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) Mus musculus (Mouse) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans Rattus norvegicus (Rat) Bacillus cereus Bacillus subtilis 
2026-08-24 | PXD072999 | Pride
Deep learning Dda proteomics Peptide-spectrum matches (psms) rescoring Dda-bert Peptide identification 
UnknownThe stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression.
Not available
S-EPMC3510239 | biostudies-literature
ProteomicsTo identify the phenol soluble modulins whose production are primarily affected by SarZ in Staphylococcus epidermidis
Phenol-soluble modulins (PSMs) are a class of short, amphipathic, α-helical peptides, which have strong cytolytic effects toward leukocytes and erythrocytes in S. epidermidis. SarZ is a key transcriptional regulator required for the expression of virulence factors. To determine whether the productio...
ORGANISM(S): Staphylococcus epidermidis RP62A 
2024-12-05 | PXD057952 | Pride
Phenol soluble modulins Staphylococcus epidermidis Lc-ms/ms 
TranscriptomicsThe stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression
The stringent response is initiated by rapid (p)ppGpp synthesis, which leads to a profound reprogramming of gene expression in most bacteria. The stringent phenotype seems to be species specific and may be mediated by fundamentally different molecular mechanisms. In Staphylococcus aureus, (p)ppGpp s...
ORGANISM(S): Staphylococcus aureus 
2013-04-05 | GSE45617 | GEO
Genomics
Pea Ridge PSMs
PRJNA1288479 | ENA
TranscriptomicsQuorum-sensing control of sepsis in the coagulase-negative staphylococcal species Staphylococcus haemolyticus
In many pathogens, quorum-sensing systems regulate virulence. Quorum-sensing is therefore often proposed as a target for antivirulence drug development. Coagulase-negative staphylococci are leading causes of nosocomial blood infections and of mortality due to sepsis as the most extreme consequence o...
ORGANISM(S): Staphylococcus haemolyticus Staphylococcus aureus subsp. aureus MW2 Staphylococcus epidermidis ATCC 12228 Chlamydia trachomatis D/UW-3/CX Coxiella burnetii Rickettsia rickettsii Chlamydia muridarum Staphylococcus epidermidis RP62A Chlamydia pneumoniae AR39 Borreliella burgdorferi B31 Coxiella burnetii RSA 493 Chlamydia caviae GPIC Staphylococcus haemolyticus JCSC1435 Granulibacter bethesdensis 
2025-09-23 | GSE285447 | GEO
GenomicsStaphylococcus aureus
The stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression
PRJNA195405 | ENA
TranscriptomicsEffect of S. epidermidis phenol-soluble modulins on primary human keratinocytes.
To investigate the effect of synthetic phenol-soluble modulins (PSMs) secreted by S. epidermidis on primary keratinocytes. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
ORGANISM(S): Homo sapiens 
2023-01-01 | GSE209653 | GEO
TranscriptomicsEvolution of virulence control by the staphylococcal agr quorum-sensing regulator
The Staphylococcus aureus accessory gene regulator (agr) is a prototype quorum-sensing system in Gram-positive bacteria and a paradigmatic example of gene regulation by a small regulatory RNA, RNAIII. Using genome-wide transcriptional profiling in the community-associated methicillin-resistant (CA-M...
ORGANISM(S): Staphylococcus aureus 
2010-05-14 | E-GEOD-10165 | biostudies-arrayexpress
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