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TranscriptomicsSLAM-seq analysis of mRNA half-lives in human CD8⁺ T cells during activation
SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing of RNA) was applied to human primary CD8⁺ T cells subjected to in vitro activation with αCD3/αCD28 beads. To quantify mRNA half-lives and their dynamic changes during CD8⁺ T cell activation, we implemented a pulse-chase design with 2...
ORGANISM(S): Homo sapiens 
2025-10-15 | E-MTAB-15648 | biostudies-arrayexpress
TranscriptomicsNascent mRNA profiling of LPS-stimulated mouse macrophages
To identify transcriptionally regulated genes in primary mouse macrophages stimulated with LPS with high sensitivity, we isolated nascent RNA following metabolic labelling with 4-thiouridine during the last 35 min before cell harvest, as recently described (Dolken et al. 2008 RNA 14:1959-72). Microa...
ORGANISM(S): Mus musculus 
2010-05-07 | E-GEOD-20674 | biostudies-arrayexpress
ProteomicsMass spectrometry approach to identify mitochondrial poly(A) RNA interacting proteins
To identify mitochondrial RNA-interacting proteins, we developed three related mass spectrometry based methods. In the first method, called mitochondrial crosslinking (MXL), mitochondria of 4-thiouridine labelled cells were isolated, exposed to UV-light and poly(A) RNA was isolated. In the second me...
ORGANISM(S): Homo sapiens (Human) 
2019-10-15 | PXD014957 | Pride
Mitochondrial rna Mass spectrometry 4-thiouridine labelling & crosslinking 
UnknownSynergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting.
Not available
S-EPMC10276402 | biostudies-literature
TranscriptomicsEffects of upf1delta on RNA stability
The Upf1 protein is a major factor in nonsense-mediated decay. We used an in vivo labelling system (Cleary et al. 2005 Nat Biotechnol. 23, 232-7) to estimate the decay rates of upf1delta and wild type cells over-expressing the transcription factor Mei4.
ORGANISM(S): Schizosaccharomyces pombe 
2013-06-03 | E-MTAB-1324 | biostudies-arrayexpress
TranscriptomicsEffect of cellular and viral miRNAs on target RNA half-life in three human B-cell lines
Total, nascent and unlabeled RNA were prepared following 1h of labeling with 100 µM 4-thiouridine and 3 replicates analyzed by Affymetrix Gene ST 1.0 arrays Transcript half-lives were determined in DG75-eGFP, DG75-10/12 and BCBL-1 based on nascent/total RNA ratios; unlabeled RNA was analyzed in addi...
ORGANISM(S): Homo sapiens 
2010-11-04 | E-GEOD-18882 | biostudies-arrayexpress
TranscriptomicsGenomewide measurements of whole embryo mRNA decay in Drosophila
whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase These TU-Decay microarrays analyze mRNA levels at three timepoints: a one hour pulse, one hour chase, and three hour chase. Measurements with or without transcription inhibition by actinomycin D (ActD) were compared.
ORGANISM(S): Drosophila melanogaster 
2015-03-31 | E-GEOD-67435 | biostudies-arrayexpress
TranscriptomicsDissecting primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression
NIH-3T3 cells were pretreated for 15 min with either DMSO (mock) or cycloheximide followed by addition of either mock, 100 U/ml IFNalpha or 100 U/ml IFNgamma for 1h. During the last 30 min, 500 µM 4-thiouridine was added to cell culture medium. Total cellular RNA was isolated using Trizol reagent an...
ORGANISM(S): Mus musculus 
2013-07-04 | E-GEOD-30457 | biostudies-arrayexpress
TranscriptomicsEffects of deletion of RNA-binding proteins on RNA stability using an in vivo labelling system to estimate the decay rates of RBP mutants and wild type S. pombe cells
To investigate the contribution of RNA-binding proteins to the regulation of RNA decay we used an in vivo labelling system (Cleary et al. 2005 Nat Biotechnol. 23, 232-7) to estimate the decay rates of RBP mutants and wild type S. pombe cells
ORGANISM(S): Schizosaccharomyces pombe 
2014-11-06 | E-MTAB-2318 | biostudies-arrayexpress
TranscriptomicsTemporal response of DCs to LPS stimulation: 4sU_sequencing
Regulation of RNA levels is critical for the response to external stimuli and determined through the interplay between RNA production, processing and degradation. Despite the centrality of these processes, most global studies of RNA regulation do not distinguish their separate contributions and rela...
ORGANISM(S): Mus musculus 
2011-04-24 | E-GEOD-25432 | biostudies-arrayexpress
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