相关实验视频

Updated: Jun 25, 2025

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

纳米孔直接RNA测序的测序精度和系统错误

Wang Liu-Wei^1,2,3, Wiep van der Toorn^4,5, Patrick Bohn⁶

¹Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany. liuwei.wang@fu-berlin.de.

|May 28, 2024

概括

直接RNA测序 (dRNA-seq) 提供全长的转录,但其准确性不够研究. 这项研究揭示了一致的错误模式,删除是常见的,富含细胞蛋白/乌拉的区域容易出现错误,影响RNA测序数据的质量.

科学领域:

基因组学就是基因组学.
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:

在牛津纳米孔技术 (ONT) 平台上的直接RNA测序 (dRNA-seq) 可实现全长的转录测序,包括修改和多A尾部信息.
尽管它有潜力,但dRNA-seq的准确性和错误概况仍然没有得到充分的描述.

研究的目的:

综合评估dRNA-seq的准确性,并在各种生物和合成RNA中描述系统错误.
识别导致序列错误的序列上下文和信号级特征.
评估不同基地呼叫者的影响,并确定数据丢失的来源.

主要方法:

使用ONT套件SQK-RNA001和SQK-RNA002.2分析来自多种物种和合成RNA的dRNA-seq数据.
系统地描述错误类型 (删除,插入,不匹配) 和它们的分布.
检查原始信号数据以将错误与序列上下文和信号特征相关联.
评估基调器性能和识别与适配器相关的错误.
使用SQK-RNA004套件生成和分析dRNA-seq数据.

主要成果:

中位数读取精度在87%至92%之间,删除是主要的错误类型.
不同聚合物和短同聚合物是主要的错误贡献者;丰富的细胞因子/尿素区域显示出更高的错误率.
在核酸和动机水平上观察到系统偏差,与信号级特征相关.
阅读质量得分部分预测错误率;未检测到的DNA适配器有助于错误.
新的SQK-RNA004套件提高了整体准确性,但保留了类似的系统错误模式.

结论:

这项研究提供了第一个对dRNA-seq错误的系统分析,揭示了可重现的模式.
识别了信号级不足和序列上下文依赖性作为错误来源.
为dRNA-seq数据开发可靠的错误校正方法奠定了基础.

关键词:

直接的RNA测序是指直接的RNA测序.史诗转录组学史诗转录组学纳米孔测序的测序在SQK-RNA004中使用.测序的准确性测序的准确性测序错误是因为测序错误.文字转录学 (Transcriptomics) 是一个学科.

更多相关视频

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

相关概念视频

RNA-seq

RNA-seq

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...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...