而PRO-seq技术就是对传统RNA-seq技术在这方面的改进,它可以富集并且测出刚刚被RNA聚合酶转录出来的新生RNA,并且精度达到一个碱基对。 相关文献:Nature protocol Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) https://www.ncbi.nlm.nih.gov/pubmed...
a At cell level (top), a reporter (orange) is expressed independently in a Tn-Seq protocol; in contrast, its initiation codon and the inverted repeats (IR) are mutated in ProTInSeq, so that the reporter is only expressed when inserted in-frame to an endogenous protein. At population leve...
NatureNature protocolsMahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, et al. Base-pair-resolution genome- wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc. 2016 Aug 1; 11(8):1455-76. https://doi.org/10.1038/nprot.2016.086 ...
PREFIX.fastq.gz were made according to PRO-seq protocol as inhttps://www.ncbi.nlm.nih.gov/pubmed/23430654UMI1 was set to 0 by default. The pipeline will NOT remove PCR duplicates. bash proseq2.0.bsh -i $bwaIndex -c $chromInfo -SE -P -T myOutput2 -O myOutput2 -I PREFIX ...
杂志:nature protocols 这篇笔记我翻译了一部分,并没有全文翻译,因为文献里有一部分是非常详细的实验步骤。有需要的同学可以自行下载参考实验步骤,本篇笔记旨在了解Pro-seq的一些背景知识。 摘要 作者提供了一个Pro-seq的protocol,和pro-cap的实验方法,这个方法可以绘制处于激活状态下的RNA聚合酶的位置(pro-seq),并且...
The nature of VSIG1-dependent genes prominently expressed by the SP suggested that VSIG1 represses calcium binding (PRKCG and SYT17), microtubule/dendrite localization (MAP2 and TUB1A1), signaling (GLI1, TAZ, PDGFA ligand, and the WNT antagonist NKD1), migration/protein trafficking (TUB1...
HIV-1 infection generally contains a high frequency of mutations and deletions in the provirus. We further investigated how sequence mismatches affect the efficiency of the HIV-DNA-capture protocol using U1 cells. These cells present a wider range of mutations when compared to the HXB2-based prob...