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MetabolomicsPROMIS, global analysis of PROtein-Metabolite Interactions using Size separation in Arabidopsis thaliana
Small molecules not only represent cellular building blocks and metabolic intermediates, but also regulatory ligands and signaling molecules that interact with proteins. Although these interactions affect cellular metabolism, growth, and development, they have been largely understudied. Herein, we d...
2018-07-19 | MTBLS94 | MetaboLights
TranscriptomicsCohesin is a key determinant of interphase chromosome domain architecture (HiC)
To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elem...
ORGANISM(S): Mus musculus 
2013-12-11 | E-GEOD-49017 | biostudies-arrayexpress
MetabolomicsA Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract
Herbal preparations are complex mixtures of natural products, many of which are able to reach the distal gut. There, they influence the microbial communities, and can be metabolized into bioactive metabolites. The aim of this study was to establish an interdisciplinary platform to unravel interactio...
2017-12-14 | MTBLS479 | MetaboLights
GenomicsCohesin is a key determinant of interphase chromosome domain architecture (ChIP-seq)
To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elem...
ORGANISM(S): Mus musculus 
2013-12-11 | E-GEOD-48938 | biostudies-arrayexpress
TranscriptomicsCohesin is a key determinant of interphase chromosome domain architecture (RNA-seq)
To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elem...
ORGANISM(S): Mus musculus 
2013-12-11 | E-GEOD-48965 | biostudies-arrayexpress
ProteomicsTime-Resolved Analysis of Protein-Protein Ensembles using a Destabilizing Domain (TRAPPED) to resolve dynamic interactions of SARS-CoV-2 nsp15
Cellular protein-protein interactions are dynamic and can change over time. Current interactomics methods capture steady-state information but lack the ability to differentiate when the interactions occur. This study developed a post-translational method for synchronizing protein accumulation that a...
ORGANISM(S): Homo sapiens (Human) 
2025-09-29 | PXD063935 | Pride
Dihydrofolate reductase Proteomics Affinity purification-mass spectrometry Interactomics Destabilizing domain Virus-host protein interactions 
ProteomicsStabilization of Interdomain Interactions in G protein α Subunits as a Determinant of Gαi Subtype Signaling Specificity
Highly homologous members of the Gαi family, Gαi1-3, have distinct tissue distributions and physiological functions, yet their biochemical and functional properties are very similar. We recently identified PDZ-RhoGEF (PRG) as a novel Gαi1 effector that is poorly activated by Gαi2. In a proteomic pro...
ORGANISM(S): Homo sapiens (Human) 
2024-03-25 | PXD050824 | Pride
Heterotrimeric g protein Proximity labeling Mass spectrometry Structure. G protein-coupled receptor Effector coupling Rho gef Domain interactions Alpha subunits 
GenomicsDeterminng global implications of the ADAR3 R-domain on mediating ADAR3-RNA interactions
Determinng global implications of the ADAR3 R-domain on mediating ADAR3-RNA interactions
PRJNA1040869 | ENA
GenomicsInteractions of CAF1-NOT complex components from Trypanosoma brucei
Our trypanosome yeast two-hybrid prey library was made by random shotgun genomic cloning. NOT2, NOT10, NOT11 and CAF40 were used as baits to screen the library by mating. Diploid progeny were subjected to selection, resulting in between 100 and 800 surviving colonies, from which inserts were amplifi...
ORGANISM(S): Trypanosoma brucei 
2022-01-14 | E-MTAB-4946 | biostudies-arrayexpress
TranscriptomicsComparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.
Topological domains are key architectural building blocks of chromosomes in complex genomes. Their functional importance and evolutionary dynamics are however not well defined. Here we performed comparative Hi-C in liver cells from four mammalian species, and characterized the conservation and dive...
ORGANISM(S): Canis lupus familiaris 
2015-02-26 | E-GEOD-65126 | biostudies-arrayexpress
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