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相关概念视频

Ribosome Profiling02:24

Ribosome Profiling

3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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相关实验视频

Updated: Jun 18, 2025

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
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pyRBDome:一个全面的计算平台,用于增强RNA结合蛋白质组数据.

Liang-Cui Chu1,2, Niki Christopoulou1,2, Hugh McCaughan1,2

  • 1Centre for Engineering Biology, University of Edinburgh, Edinburgh, UK.

Life science alliance
|July 30, 2024
PubMed
概括

我们开发了pyRBDome,这是一个计算管道,以提高RNA结合蛋白质组数据质量. 它提高了识别RNA结合蛋白和序列的准确性,减少了实验噪声,增加了对结果的信心.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Last Updated: Jun 18, 2025

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An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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科学领域:

  • 分子生物学分子生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 高通量蛋白质组学方法已经推进了RNA结合蛋白 (RBPome) 和RNA结合序列 (RBDome) 的识别.
  • 在这些大型数据集中,量化噪声,例如假阳性,由于低通量验证方法的存在,具有挑战性.

研究的目的:

  • 引入pyRBDome,这是一个in silico管道,旨在提高RNA结合蛋白质组数据的精度和可靠性.
  • 改进真正的RNA结合蛋白和RNA结合部位的识别.

主要方法:

  • pyRBDome 将实验性的 RBPome/RBDome 数据与来自机器学习工具的 RNA 结合位点 (RBS) 预测集成在一起.
  • 它结合了高分辨率的结构数据,并使用统计评估来改进数据.
  • 使用pyRBDome结果训练了新的整体机器学习模型,以提高RBS检测灵敏度和特异性.

主要成果:

  • pyRBDome 便于在实验数据集中快速识别可能的真实RNA结合剂.
  • 对人类RBDome数据的分析显示,在高分辨率结构中,紫外线交联部位和实际RNA结合之间存在差异.
  • 该管道在检测RNA结合位点方面表现出增强的灵敏度和特异性.

结论:

  • pyRBDome提供了一种强大的计算方法,以增加对RNA结合蛋白质组和序列数据集的信心.
  • 它解决了使用结构数据作为RNA结合验证的唯一基准的局限性.
  • 该管道是研究人员使用RBPome和RBDome数据的宝贵工具.