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ProteomicsCodon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
This study investigates the immediate effects of single, double, and triple branched-chain amino acid (BCAA) deprivation on translational dynamics in NIH3T3 cells. Using a multi-omics approach combining RNA-seq, ribosome profiling (Ribo-seq), quantitative proteomics, and tRNA charging assays, we sys...
ORGANISM(S): Mus musculus (Mouse) 
2025-09-13 | PXD067949 | Pride
Proteomics Elongation bottleneck Nutrient stress response Mass spectrometry Nih3t3 cells Ribosome profiling Amino acid starvation Translation regulation Trna charging Codon-specific stalling 
TranscriptomicsTranscription profiling of Drosophila CA/AA time series of y w
Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the pr...
ORGANISM(S): Drosophila melanogaster 
2008-06-14 | E-GEOD-6490 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Drosophila AA1/AA2 time series of cn bw
Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the pr...
ORGANISM(S): Drosophila melanogaster 
2008-06-14 | E-GEOD-6492 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Drosophila CA/AA time series of y w tim01
Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the pr...
ORGANISM(S): Drosophila melanogaster 
2008-06-14 | E-GEOD-6493 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Drosophila second CA/AA time series of y w
Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the pr...
ORGANISM(S): Drosophila melanogaster 
2008-06-14 | E-GEOD-6491 | biostudies-arrayexpress
GenomicsGenome-Wide And Phase-Specific DNA-Binding Rhythms Of BMAL1 Control Circadian Output Functions In Mouse Liver
Using chromatin immuno-precipitation (ChIP) combined with deep sequencing (ChIP-seq) we obtained a time resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed to identify over two thousand binding sites with peak binding narrowly centered around Zeitgeber time (ZT) 6. Annotation...
ORGANISM(S): Mus musculus 
2011-02-23 | E-GEOD-26602 | biostudies-arrayexpress
UnknownEmpirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.
Not available
S-EPMC115253 | biostudies-literature
GenomicsThe telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
The majority of Saccharomyces cerevisiae snoRNA promoters contain an aRCCCTaa sequence motif located at the upstream border of a TATA-containing nucleosome-free region. Genome-wide ChIP-seq analysis showed that these motifs are bound in vivo by Tbf1, a telomere-binding protein known to recognize mam...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-28 | E-GEOD-20870 | biostudies-arrayexpress
TranscriptomicsCIRP, a cold-inducible RNA-binding protein, modulates circadian gene expression posttranscriptionally
In mammalian tissues circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. Here we show that simulated body temperature cycles, but not peripheral oscillators, can control the rhythmic expression of Cold-In...
ORGANISM(S): Mus musculus 
2012-08-24 | E-GEOD-37685 | biostudies-arrayexpress
TranscriptomicsCircadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver [RNASeq]
Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. While rhythmic mRNA accumulation has been extensively studied, comparatively less is known ab...
ORGANISM(S): Mus musculus 
2015-11-10 | E-GEOD-73552 | biostudies-arrayexpress
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