7. Xue Y, Zhou Y, Wu T, et al. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping[J]. Molecular cell, 2009, 36(6): 996-1006. 编辑于 2024-03-25 18:47・IP 属地上海 ...
2014. RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins . Genome Biol 15 : R7.Lu Z, Guan X, et al. RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins. Genome Biol. 2014;15...
不过一般不用指定--extsize 200,--shift 100采用自动建模,除非明确知道RNA fragment长度。 5.Differential m6A level analysis 首先将2个肿瘤中narrow peak有重叠的区域合并,没有重叠的也保留(bedtools merge),合起来作为一个reference m6A peaks list,然后用bedtools 的multicov工具去计算input组和tumor组在这个区域...
we performed RIP-seq analysis of individual subunits of the canonical Sm ring. We also performed RIP-seq on Trailer Hitch (Tral), a protein that contains an Sm domain (Figure1c). Tral is not incorporated into the canonical Sm ring; therefore, we expected it to associate...
Cross-linking and analysis of cDNA (CRAC) 带有抗体的RBPs的免疫沉淀需要自然条件。使用不依赖蛋白质-肽相互作用的亲和树脂可以在变性条件下进行严格的洗涤步骤。这种方法被称为CRAC (Cross-linking and analysis of cDNA),由David Tollervey的实验室开发,用于研究酵母中snoRNP组分(Nop1、Nop56、Nop58和Rrp9)的...
produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the ide...
Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-...
RIP-Seq analysis of non-PPR chloroplast editing factors reveals broad RNA interactions and enrichment of less efficiently translated RNAs by OZ1 and ORRM1 ... C-to-U RNA editing in angiosperm chloroplasts requires a large suite of proteins bound together in the editosome. The editosome is compr...
CRAC（Cross-linking and analysis of cDNA）方法提供了一种在变性条件下纯化RBPs的RNA复合物的替代方案，用于研究酵母中snoRNP组分的RNA-蛋白相互作用。这项技术也被应用于研究核糖体生物发生的结构特征，包括识别RNA螺旋酶Prp43和核糖体组装因子的结合位点。PAR-CLIP（Photoactivatable-ribonucleoside-enhanced ...
produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the ide...