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ProteomicsComparison of the transcriptome, translatome and proteome response to diurnal oscillations in cyanobacteria
The aim of this study was to find the cause for the previously reported inconsistency between oscillating transcription and constant protein levels under day-night growth conditions in cyanobacteria. To determine whether translational regulation counteracts transcriptional changes, Synechocystis sp....
ORGANISM(S): Synechocystis sp. PCC 6803 substr. GT-I 
2021-09-10 | PXD023812 | Pride
Shotgun proteomics Msgf+ Protein turnover Dyanobacteria Openms Diurnal gene expression Post-transcriptional regulation Metabolic regulation Data-dependent acquisition 
ProteomicsInvestigation of protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator
The aim of this study was to understand how autotrophic (CO2-fixing) bacteria balance the different needs for substrate assimilation, growth functions, and resilience in order to thrive in their environment.To this end, the proteome of the model chemolithoautotroph Ralstonia eutropha a.k.a. Cupriavi...
ORGANISM(S): Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha) 
2022-02-17 | PXD024819 | Pride
Cupriavidus necator Shotgun proteomics Resource balance Msgf+ Cellular economy Openms Substrate limitation Ralstonia eutropha Resource allocation Data-dependent acquisition 
ProteomicsProteome allocation strategies under nutrient-limiting conditions in the cyanobacterium Synechocystis
The response of the model cyanobacterium Synechocystis sp. PCC6803 towards light and carbon limitation was systematically probed. To this end, Synechocystis sp. PCC6803 was cultivated in a photo-bioreactor driven in turbidostat-mode. The turbidostat is a continuous cultivation that enabled cells to ...
ORGANISM(S): Synechocystis sp. PCC 6803 substr. GT-S 
2018-09-12 | PXD009582 | Pride
Shotgun proteomics Cyanobacteria Msgf+ Cellular economy Carbon limitation Openms Resource allocation Data-dependent acquisition Light limitation 
ProteomicsA Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections
Long term-catheterization leads inevitably to a catheter-associated bacteriuria caused by multispecies bacterial biofilms growing on and in the catheters. The overall goal of the presented study was (I) to unravel bacterial community structure and function of such an uropathogenic biofilm and (II) t...
ORGANISM(S): Morganella <scale Insect> (ncbitaxon:108061) Morganella <fungus> (ncbitaxon:90690) Pseudomonas Sp. (ncbitaxon:306) Homo Sapiens (ncbitaxon:9606) 
2016-07-19 | MSV000079927 | MassIVE
TranscriptomicsThe classical histone deacetylases FfHdF1 and FfHdF2 are both major regulators of secondary metabolism in Fusarium fujikuroi
Histone modifications have been shown to be crucial for secondary metabolism in various filamentous fungi. Here we studied the influence of histone acetylation on secondary metabolite production in the phytopathogenic fungus Fusarium fujikuroi, a known producer of several secondary metabolites inclu...
ORGANISM(S): Fusarium fujikuroi 
2013-10-05 | E-GEOD-43768 | biostudies-arrayexpress
UnknownGene Flow Across Genus Barriers - Conjugation of Dinoroseobacter shibae's 191-kb Killer Plasmid into Phaeobacter inhibens and AHL-mediated Expression of Type IV Secretion Systems.
Not available
S-EPMC4886583 | biostudies-literature
ProteomicsS. aureus COL anaerobiosis absolute protein quantification
Absolute protein quantification was applied to follow the dynamics of the cytoplasmic proteome of Staphylococcus aureus in response to long-term oxygen starvation. For 1,168 proteins, the majority of all expressed proteins, molecule numbers per cell have been determined to monitor the cellular inves...
ORGANISM(S): Staphylococcus aureus (strain COL) 
2016-07-11 | PXD000330 | Pride
Absolute protein quantification Lc-mse Anaerbiosis Synapt Lc-imse Staphylococcus aureus 
GenomicsInferring expressed genes by whole-genome sequencing of plasma DNA
The analysis of cell-free DNA (cfDNA) in plasma represents a rapidly advancing field in medicine. cfDNA consists predominantly of nucleosome-protected DNA shed into the bloodstream by cells undergoing apoptosis. We performed whole-genome sequencing (WGS) of plasma DNA and identified two discrete reg...
EGAS00001001754 | EGA
ProteomicsFOXP1 is a transcriptional Coactivator of Wnt/β-catenin signaling in Diffuse Large B-cell Lymphoma
We used a mass spectrometry-coupled lentiviral ‘CD-tagging’ mutagenesis approach to identify genes that activate Wnt/β-catenin signaling. Human A375 melanoma cells containing a β-catenin-driven GFP (green fluorescent protein) transcriptional reporter were transduced with CDBF lentivirus. When integr...
ORGANISM(S): Homo sapiens (Human) 
2016-07-05 | PXD001485 | Pride
Flag apms Gain-of-function screening Wnt signaling Foxp1 
Genomicsena-DATASET-MUG-24-06-2016-10:36:41:861-335 - samples
Merged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments.
EGAD00001002217 | EGA
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