Run-on法是将核酸类似物添加到样品中,从而使nascent RNA能够从总的RNA混合物中进行富集,并能够检测瞬时RNA的转录(FIG. 4a)。全局run-on测序(Global run-on sequencing, GRO-seq)与精确核酸run-on测序(Precision nuclear run-on sequencing, PRO-seq)是分别将Bru或生物素修饰的核酸在RNA的转录期整合到nascent RNA...
Unlike in RNA-seq, these spike-ins are not standardized and, in many cases, depend on a run-on reaction that is assumed to have constant efficiency across samples. To assess the validity of this assumption, we analyze a large number of published nascent RNA spike-ins...
The high reaction efficiency permits AMUC‐seq directly and efficiently to recover nascent RNA information from total RNAs. AMUC‐seq is validated by being used to detect mRNA half‐lives and investigating the direct gene targets of a G‐quadruplex stabilizer, which can be regarded as potential ...
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...
Single-cell nascent RNA sequencing unveils coordinated global transcription Article Open access 05 June 2024 grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis Article Open access 15 June 2023 References Liu, Y., Beyer, A. & Aebersold, R. On the dependency of ...
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 ...
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
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
Measuring Nascent Transcripts by Nascent-seq 来自 Semantic Scholar 喜欢 0 阅读量: 57 作者:XC Fei,SA Marshall,D Yu,T Sun 摘要: A complete understanding of transcription and co-transcriptional RNA processing events by polymerase requires precise and robust approaches to visualize polymerase progress ...
RSeQC - Various RNA-seq QC metrics Preseq - Estimation of library complexity BBMap - Analyzes the sequencing coverage Coverage Graphs Create bedGraph coverage files (BEDTools Create bigWig coverage files (deeptools) Transcript identification HOMER GroHMM PINTS Quantification of Genes and Nascent Transc...