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TranscriptomicsIdentifying transcription start sites and active enhancer elements using BruUV-seq
BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription rea...
ORGANISM(S): Homo sapiens 
2015-12-21 | E-GEOD-75398 | biostudies-arrayexpress
TranscriptomicsRate of elongation by RNA polymerase II is influenced by specific gene features and histone modifications
The rate of transcription elongation plays important roles in the timing of expression of full-length transcripts as well as for the regulation of alternative splicing. In this study we coupled Bru-Seq technology with 5,6-dichlorobenzimidazole 1-M-NM-2-D-ribofuranoside (DRB) to estimate the elongati...
ORGANISM(S): Homo sapiens 
2014-04-01 | E-GEOD-55534 | biostudies-arrayexpress
TranscriptomicsGenome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin
The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a M-bM-^@M-^\cleavable complexM-bM-^@M-^]. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment aff...
ORGANISM(S): Homo sapiens 
2013-10-29 | E-GEOD-48678 | biostudies-arrayexpress
TranscriptomicsCoordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response
Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, miRNAs, and RNA-binding proteins. Here, we present Bru-Seq and BruChase-Seq to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeosta...
ORGANISM(S): Homo sapiens 
2013-01-29 | E-GEOD-43440 | biostudies-arrayexpress
UnknownCo-transcriptional splicing efficiencies differ within genes and between cell types.
Not available
S-EPMC8208053 | biostudies-literature
TranscriptomicsEffects of physiological and synthetic IAP antagonism on c-IAP dependent signaling
Cellular inhibitor of apoptosis proteins 1 and 2 (c-IAP1/2) play central roles in signal transduction mediated by numerous receptors that participate in inflammatory and immune responses. In certain pathways, such as activation of NF-kB, their degradation is a major regulatory event and is physiolog...
ORGANISM(S): Homo sapiens 
2015-02-09 | E-GEOD-64927 | biostudies-arrayexpress
UnknownTranscriptional and post-transcriptional regulation of nucleotide excision repair genes in human cells.
Not available
S-EPMC4531258 | biostudies-literature
UnknownUse of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA.
Not available
S-EPMC4009065 | biostudies-literature
TranscriptomicsBru-seq nascent RNA sequencing of human and mouse cells: correlation to replication timing and genome instability
Bru-seq nascent RNA sequencing (PubMed ID 23973811) was performed on two primary human fibroblast cell lines, mouse embryonic stem cells, and GM12878 human lymphoblastoid cells. Read data, which include both exon and intron signals, were used to identify transcription unit spans genome-wide, where a...
ORGANISM(S): Homo sapiens 
2014-10-17 | E-GEOD-55862 | biostudies-arrayexpress
Unknown1730. Outcomes of Patients With Detectable Cytomegalovirus (CMV) DNA at Randomization in the Double-blind, Placebo-Controlled Phase 3 Trial of Letermovir (LET) Prophylaxis for CMV-Seropositive Allogeneic Hematopoietic-Cell Transplantation (HCT) Recipients
Not available
S-EPMC6252851 | biostudies-literature
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