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TranscriptomicsWide-spread disruption of transcription termination in HSV-1 infection: Next generation sequencing of total and newly transcribed (4sU-RNA) RNA
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. N...
ORGANISM(S): Homo sapiens 
2015-05-26 | E-GEOD-59717 | biostudies-arrayexpress
TranscriptomicsWide-spread disruption of transcription termination in HSV-1 infection: Next-generation sequencing of translational activityd by ribosome profiling
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science...
ORGANISM(S): Homo sapiens 
2015-05-26 | E-GEOD-60040 | biostudies-arrayexpress
Proteomics,Multiomicsp53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-05-24 | MSV000079767 | MassIVE
Otherp53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses.
Data from ProteomeXchange, PXD ID: PXD001976. File: ELITE-RSLC001392.mzml. Published as part of . From the Abstract: {{i}} We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino a...
ORGANISM(S): Homo_sapiens_viruses, Human 
GPM32320017018 | GPMDB
Resource Reanalysis 
TranscriptomicsDerivation and maintenance of murine trophoblast stem cells under defined conditions
Trophoblast stem (TS) cells are in vitro equivalents to the precursor cells of the placenta. In mice, TS cells can be derived either from polar trophectoderm (TE) of blastocyst outgrowths or from postimplantation extraembryonic ectoderm (ExE), originating from polar TE. Since their first successful ...
ORGANISM(S): Mus musculus 
2014-01-28 | E-GEOD-47719 | biostudies-arrayexpress
TranscriptomicsUltra short and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
RNA synthesis and decay rates determine the steady-state levels of cellular RNAs. Metabolic tagging of newly transcribed RNA by 4-thiouridine (4sU) can reveal the relative contributions of RNA synthesis and decay rates. The kinetics of RNA processing, however, so far remained unresolved. Here, we sh...
ORGANISM(S): Homo sapiens 
2012-04-25 | E-GEOD-31653 | biostudies-arrayexpress
TranscriptomicsReal-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection
During viral infections cellular gene expression is subject to rapid alterations induced by both viral and antiviral mechanisms. In this study, we applied metabolic labeling of newly transcribed RNA with 4-thiouridine (4sU-tagging) to dissect the real-time kinetics of cellular and viral transcriptio...
ORGANISM(S): Mus musculus 
2013-02-14 | E-GEOD-35833 | biostudies-arrayexpress
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