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MetabolomicsVirus-induced codon-specific reprogramming to favor viral RNA translation
Recent evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons remains a puzzling question. Using ribosome footprinting, here we analysed ...
2025-06-16 | MTBLS2443 | MetaboLights
MetabolomicsRNA modification dynamics during Enterococcus faecalis OG1RF growth
Quantitative analysis of relative levels of RNA modifications in small (primarily tRNA) and large (primarily 16S/23S rRNA) RNAs isolated from Enterococcus faecalis OG1RF across a growth time course in BHI media.
2026-08-20 | MTBLS14602 | MetaboLights
MetabolomicsTranslational repression of viral RNA mediates arbovirus persistence in mosquitoes

Persistent infection of mosquito vectors is essential for the transmission of arboviruses, yet how these viruses produce sufficient progeny without compromising host cell fitness remains unclear. Arbovirus genomes exhibit suboptimal codon usage for both human and mosquito hosts, raising questions...

2026-02-12 | MTBLS12760 | MetaboLights
ProteomicsRNA oligomers training set for the Pytheas scoring function
Mass spectrometry remains an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids i...
ORGANISM(S): Escherichia coli 
2022-05-04 | PXD030435 | Pride
Training set Scoring function Rna Pytheas 
TranscriptomicsBovine pre-transfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer (endometrial study)
The aberrant gene expression in the uterine endometrium and embryo has been the major causes of pregnancy failure in cattle. Therefore, selecting cows having adequate endometrial receptivity and embryos of better developmental competence based on the gene expression could increase the number of calv...
ORGANISM(S): Bos taurus 
2010-04-07 | E-GEOD-20974 | biostudies-arrayexpress
TranscriptomicsTransfer of Non-coding DNA Drives Regulatory Rewiring in Bacteria
The rapid pace of evolution in bacteria is widely attributed to the promiscuous horizontal transfer and recombination of protein-coding genes. However, it is not known whether the same forces also drive the evolution of non-coding regulatory regions. Here we demonstrate that regulatory region can M-...
ORGANISM(S): Escherichia coli CFT073 
2014-11-04 | E-GEOD-59468 | biostudies-arrayexpress
ProteomicsSwapped genetic code block viral infections and gene transfer
Removing cellular transfer RNAs (tRNAs), making their cognate codons unreadable, creates a genetic firewall that prevents viral replication and horizontal gene transfer. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus, including tRNAs, potentially re...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) 
2022-07-08 | MSV000089854 | MassIVE
TranscriptomicsResponse of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.
The global gene expression program that accompanies the adaptation of Saccharomyces cerevisiae to an abrupt transfer from a fermentable to a nonfermentable carbon source was characterized by using a cDNA microarray to monitor the relative abundances and polysomal distributions of mRNAs. Features of ...
ORGANISM(S): Saccharomyces cerevisiae 
2005-08-25 | E-GEOD-3190 | biostudies-arrayexpress
TranscriptomicsCMV-Specific CD8+ Memory T Cells Re-Emerge After Viral Challenge And Recapitulate CMV Immunity Under Various Adoptive Transfer Conditions
Reconstitution of cytomegalovirus (CMV)-specific immunity following transplant remains a primary clinical objective to prevent CMV disease, and adoptive immunotherapy of CMV-specific T cells can be an effective therapeutic approach. Due to the persistence of CMV, most CMV-specific CD8+ T cells becom...
ORGANISM(S): Mus musculus 
2015-01-28 | E-GEOD-61927 | biostudies-arrayexpress
ProteomicsLC-MSMS nucleoside analysis of Staphylococcus aureus RNA
Staphylococcus aureus is a Gram-positive opportunistic pathogenic bacterium responsible for a broad spectrum of diseases, ranging from mild skin infections to life-threatening septicemia. Its remarkable capacity to withstand diverse and hostile environments, including antibiotic pressure and host im...
ORGANISM(S): Staphylococcus aureus 
2026-09-07 | PXD071097 | Pride
Lc-msms Rna modifications Staphylococcus aureus 
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