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MetabolomicsSuboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil’s Hole, Bermuda
Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ m...
2024-02-27 | MTBLS8122 | MetaboLights
MetabolomicsMetabolites from surface seawater collected in Narragansett Bay
In aquatic environments, the production and consumption of organic compounds is directly tied to the metabolic potential of the in situ microbial community. The community’s metabolic potential can be assessed using metatranscriptomics, which is a measure of gene expression in the environment. More r...
2016-01-14 | MTBLS293 | MetaboLights
TranscriptomicsSurface topography enhances differentiation of mesenchymal stem cells towards osteogenic and adipogenic lineages
Surface topography impacts on cell growth and differentiation, but it is not trivial to generate defined surface structures and to assess the relevance of specific topographic parameters. In this study, we have systematically compared in vitro differentiation of mesenchymal stem cells (MSCs) on a va...
ORGANISM(S): Homo sapiens 
2018-09-20 | E-MTAB-7177 | biostudies-arrayexpress
ProteomicsA Chemical Proteomics Approach for Global Mapping of Functional Lysines on Cell Surface of Living Cell
Cell surface proteins are responsible for many crucial physiological roles, and they are also the major category of drug targets as the majority of therapeutics target membrane proteins on the surface of cells to alter cellular signaling. How-ever, despite its great significance, ligand discovery ag...
ORGANISM(S): Homo Sapiens 
2024-03-01 | PXD042888 |
TranscriptomicsSurface Topography Enhances Differentiation of Mesenchymal Stem Cells Towards Osteogenic and Adipogenic Lineages
Surface topography impacts on cell growth and differentiation, but it is not trivial to generate homogeneous surface structures and to define the specific morphological parameters of relevance. In this study, we have compared gene expression profiles of mesenchymal stem cells (MSCs) on nanostructure...
ORGANISM(S): Homo sapiens 
2015-08-25 | E-GEOD-61113 | biostudies-arrayexpress
TranscriptomicsSurface topography guides morphology and spatial patterning of induced pluripotent stem cell colonies
The relevance of topographic cues for commitment of induced pluripotent stem cells (iPSCs) is largely unknown. In this study, we demonstrate that groove-ridge structures with a periodicity in the submicrometer range induce elongation of iPSC colonies, guide the orientation of apical actin fibers, an...
ORGANISM(S): Homo sapiens 
2018-10-31 | E-MTAB-7327 | biostudies-arrayexpress
TranscriptomicsUstilago maydis gene expression after growth on hydrophobic surface plus/minus hydroxy fatty acids
Infection-related development of phytopathogenic fungi is initiated by sensing and responding to plant surface cues. This response results in the formation of specialized infection structures, so-called appressoria. To unravel the program inducing appressoria in the biotrophic smut fungus Ustilago m...
ORGANISM(S): Ustilago maydis 
2014-07-23 | E-GEOD-53947 | biostudies-arrayexpress
ProteomicsGrowth condition-dependent cell surface proteome analysis of Enterococcus faecium
Using a proteolytic shaving approach we identified differentially expressed surface exposed proteins of E. faecium cells after growth in different conditions.
ORGANISM(S): Enterococcus Faecium E1162 (ncbitaxon:535206) 
2015-07-07 | MSV000079184 | MassIVE
ProteomicsStructural surfaceomics of myeloma models to identify tumor-specific protein conformations
Proteins at the cell surface are promising targets for cancer immunotherapies. While standard surface proteomics can be powerful for target discovery, even more fruitful is identifying cancer-specific surface protein features. To this end, we recently described a technology to identify cancer-specif...
ORGANISM(S): Homo sapiens (Human) 
2025-10-20 | PXD059495 | Pride
Cell surface proteomics  xl-ms  crosslinking mass spectrometry  structural biology  protein structure 
ProteomicsStructure-guided development of chemically tailored peptide binders of RNF43/ZNRF3 to enable versatile design of membrane protein-targeting PROTACs
Targeted membrane protein degradation using cell surface E3 ligases RNF43/ZNRF3 via proteolysis targeting chimeras (PROTACs) represents an effective strategy for treating membrane drug targets that cannot be fully inhibited using traditional inhibitors. Several ingenious chimeras have been developed...
ORGANISM(S): Homo Sapiens 
2025-03-04 | PXD061425 |
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