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ProteomicsConstruction, debugging and iterative redesign of synXVI, a 903-kb synthetic chromosome of Saccharomyces cerevisiae
Assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project is described. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-05-07 | PXD058199 | Pride
Yeast 2.0 Scramble Synthetic genome Yeast 
TranscriptomicsCoordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response
Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, miRNAs, and RNA-binding proteins. Here, we present Bru-Seq and BruChase-Seq to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeosta...
ORGANISM(S): Homo sapiens 
2013-01-29 | E-GEOD-43440 | biostudies-arrayexpress
TranscriptomicsGene expression response to copper toxicity between coastal and open ocean strains of marine Synechococcus
Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an o...
ORGANISM(S): Synechococcus sp. CC9311 
2010-05-17 | E-GEOD-13910 | biostudies-arrayexpress
TranscriptomicsPtrA is required for coordinate regulation of gene expression during phosphate depletion in a marine Synechococcus
The genome of the marine Synechococcus sp. WH8102 displays a minimal regulatory network yet physiological and molecular responses of this organism are tuned to episodic limitation for nitrogen and phosphorus. Microarray analyses have demonstrated a key role for the two-component regulatory system, P...
ORGANISM(S): Synechococcus sp. WH 8102 
2010-04-08 | E-GEOD-18511 | biostudies-arrayexpress
TranscriptomicsMicroarray analysis of phosphate regulation in Synechococcus sp. WH8102
Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria Synechococcus sp.WH8102, are often limited by low inorganic phosphate (P). To observe how this organism copes with P starvation, we constructed a full genome microarray and examined differences in ge...
ORGANISM(S): Synechococcus sp. WH 8102 
2010-05-18 | E-GEOD-13170 | biostudies-arrayexpress
UnknownGoblet Cell Loss Linked to NOD2 and Secondary Resection in Crohn's Disease Is Induced by Dysbiosis and Epithelial MyD88.
Not available
S-EPMC12506532 | biostudies-literature
ProteomicsInteractions between host and gut microbiota following dietary interventions
Increasing the consumption of dietary fibre has been proposed to alleviate the progression of non-communicable diseases such as obesity, type 2 diabetes and cardiovascular disease, yet the effect of dietary fibre on host physiology remains unclear. In this study, we performed a multiple diet feeding...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-08 | PXD014132 | Pride
Short chain fatty acids Gut microbiota Liver proteome C57bl/6j mice - dietary fibre modification Correlation network analysis Muc2 glycosylation 
UnknownConstruction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome.
Not available
S-EPMC11747415 | biostudies-literature
TranscriptomicsOpen Ocean and Coastal Strains of Marine Synechococcus display distinctly different Global Responses to DNA Damaging Agents
We have looked at the transcriptional response of well characterised Synechococcus open ocean (WH8102) and coastal (CC9311) isolates to two DNA damaging agents, mitomycin C and ethidium bromide, using whole genome expression microarrays. The coastal strain, which was able to grow on higher concentr...
ORGANISM(S): Synechococcus sp. WH 8102 
2013-08-01 | E-GEOD-39818 | biostudies-arrayexpress
TranscriptomicsInactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences
The GacS/GacA signal transduction system is a central regulator in Pseudomonas spp., including the biological control strain P. fluorescens Pf-5, in which GacS/GacA controls the production of secondary metabolites and exoenzymes that suppress plant pathogens. A whole genome oligonucleotide microarra...
ORGANISM(S): Pseudomonas fluorescens Pf-5 
2010-03-03 | E-GEOD-16898 | biostudies-arrayexpress
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