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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
ProteomicsSystematic characterization of 21 post-translational modification using synthetic peptides
The data presented in this study in the - context of the ProteoemTools project - is based on the synthesis of about 5000 synthetic peptides carrying 21 different post-translational modifications to systematically characterize their chromatographic and mass spectrometric properties using multimodal L...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-04-05 | MSV000091649 | MassIVE
TranscriptomicsProbing nucleosome function: A highly versatile library of synthetic histone H3 and H4 mutants
The structural integrity of the nucleosome is central to regulation of DNA metabolism and transcription. We describe a library of 486 systematic histone H3 and H4 substitution and deletion mutants in Saccharomyces cerevisiae that probe the contribution of each residue to nucleosome function and can ...
ORGANISM(S): Saccharomyces cerevisiae 
2008-09-18 | E-GEOD-10860 | biostudies-arrayexpress
TranscriptomicsExpression data from the partially synthetic yeasts SynIXR-1D, -6B, -22D, and controls.
We have replaced the right arm of chromosome IX in Saccharomyces cerevisiae with a synthetic version to generate synIXR haploids. The synthetic chromosome features multiple sequeunce modifications. We analyzed gene expression by microarray analysis in three synIXR haploids (1D, 6B, and 22D) to dete...
ORGANISM(S): Saccharomyces cerevisiae 
2011-09-13 | E-GEOD-31326 | biostudies-arrayexpress
TranscriptomicsRNA expression analysis of cells producing the synthetic protein DX over a 4hr time course
We expressed the man-made protein DX in E. coli cells over the course of 4 hours and examined effects on global gene expression. We analyzed the change in RNA expression profiles of E. coli cells expressing the synthetic protein DX every half-hour over a four hour experiment. These samples were com...
ORGANISM(S): Escherichia coli 
2010-07-21 | E-GEOD-17568 | biostudies-arrayexpress
TranscriptomicsTemporal RNASeq of C. difficile cultured within synthetic multispecies biofilm relative to C. difficile monoculture biofilms.
This experiment was performed largely to capture the dynamic transcriptional changes occurring in C. difficile when cultured within a 9 species synthetic gut communal consortium over a 48 h time series when cultured as a biofilm in vitro.
ORGANISM(S): Clostridioides difficile 
2026-09-23 | E-MTAB-15646 | biostudies-arrayexpress
ProteomicsSynthetic (Phospho)Peptide Library
The submitted dataset contains raw files from 96 synthetic peptide libraries, using either HCD or ETD as fragmentation technique. The synthesized 96 tryptic peptide libraries containing >100,000 unmodified peptides plus their corresponding >100,000 phosphorylated counterparts with precisely known s...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-04-14 | MSV000091718 | MassIVE
ProteomicsSystematic characterization of 21 post-translational modification using synthetic peptides
The data presented in this study in the - context of the ProteoemTools project - is based on the synthesis of about 5000 synthetic peptides carrying 21 different post-translational modifications to systematically characterize their chromatographic and mass spectrometric properties using multimodal L...
ORGANISM(S): Homo sapiens (Human) 
2018-06-04 | PXD009449 | Pride
Post-translational modification Acetylation Immonium ion Ptm Proteometools Synthetic standard Phosphorylation Diagnostic ion Neutral loss Synthetic peptides 
TranscriptomicsPost-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (Validation 1)
Modification of microRNA sequences by the 3' addition of nucleotides to generate so-called M-bM-^@M-^\isomiRsM-bM-^@M-^] adds to the complexity of miRNA function, with recent reports showing that 3' modifications can influence miRNA stability and efficiency of target repression. Here we show that th...
ORGANISM(S): synthetic construct 
2011-06-15 | E-GEOD-26916 | biostudies-arrayexpress
TranscriptomicsInfluence of RNA Labeling on Expression Profiling of MicroRNAs
Several technical parameters are now being optimized for microRNA expression profiling experiments, but the finite amount of total RNA available continues to bottleneck clinical investigations. We used microarrays to determine the influence of the labeling reagent on total RNA requirements and data ...
ORGANISM(S): synthetic construct 
2012-05-21 | E-GEOD-30045 | biostudies-arrayexpress
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