通过专门针对RNAs的3’末端(仅最近拉RNA聚合酶的新转录的RNA)的方法,瞬时转录组测序(transient transcriptome sequence, TT-seq)与硫醇(SH, thiol)连接的烷基化RNA代谢测序(thiol(SH)-linked alkylation for metabolic sequencing of RNA, SLAM-seq)能够降低来源于5’RNA的信号。TT-seq将标记时间限制在5分钟,因此只...
RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale ...
is a more direct and reliable indicator of enhancer activity [32,33,34,35]. Because eRNAs are often unstable, traditional transcriptome profiling such as RNA-seq cannot successfully capture these transcripts [36]. GRO/PRO-seq, which directly maps elongation-competent RNA...
et al. Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161, 526–540 (2015). This study applies NET-seq to human cells using antibodies to Ser5-phosphorylated, Ser2-phosphorylated and unphosphorylated Pol II CTD, demonstrating the positions of different...
K. From reads to genes to pathways: differential expression analysis of RNA-seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438 (2016). PubMed PubMed Central Google Scholar Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change ...
Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow for GRO-seq, PRO-seq, and ChRO-seq data. PEPPR
The starting material for RNA sequencing (RNA-seq) studies is usually total RNA or polyA+ RNA. Both forms of RNA represent heterogeneous pools of RNA molecules at different levels of maturation and processing. Such heterogeneity, in addition to the biase
<abstract abstract-type="key-points"><sec>ObjectiveDetection and quantification of RNA synthesis in cells is a widely used technique for monitoring cell viability, health, and metabolic rate.After exposure to environmental stimuli, both
sRNA-seq and mRNA-seq sample preparation For sRNA-seq, total RNA was isolated from cells treated with scrambled shRNA (as control) and shDicer cells for 7 days using the miRVana miRNA Isolation Kit (Thermo Fisher Scientific). Quality of purified RNA was confirmed with R...
relying on reverse transcription or amplification, the sample is sequenced directly through nanopores to reveal the native context of nascent RNA. nano-COP identifies both active transcription sites and splice isoforms of single RNA molecules during synthesis, providing insight into patterns of intron ...