相关实验视频
Updated: Jul 4, 2025
11:26
Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
13.7K
用纳米孔直接RNA测序进行m6A分析的计算方法的基准测试
Simone Maestri1, Mattia Furlan1, Logan Mulroney1,2,3
1Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy.
Briefings in bioinformatics
|January 27, 2024
概括
NanOlympicsMod对使用本地RNA (dRNA-seq) 的直接纳米孔测序检测N6-甲基氨酸 (m6A) 的14种工具进行了基准测试. 工具的性能各不相同,突出了对标准化基准测试的需要,以改善RNA修饰的特征.
科学领域:
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 计算生物学 计算生物学
- 在RNA生物学,RNA生物学.
背景情况:
- N6-甲基氨酸 (m6A) 是一种普遍存在的内部mRNA修饰,调节各种生物过程.
- 原生RNA (dRNA-seq) 的直接纳米孔测序是m6A识别的关键技术.
- 现有的m6A检测软件需要跨物种和参考数据集进行独立的基准测试.
研究的目的:
- 开发和验证NanoOlympicsMod,一个Nextflow管道,用于在dRNA-seq数据上比较m6A检测工具.
- 为m6A工具执行和分析提供简化计算工作流.
- 用合成和生物dRNA-seq数据集评估14m6A检测工具的性能.
主要方法:
- 开发了NanOlympicsMod,这是一个容器化的Nextflow管道,用于m6A工具的基准测试.
- 在已知的m6A位置的体外合成寡头上测试了NanOlympicsMod.
- 评估了来自酵母,小鼠和人类野生型和m6A枯竭样本的dRNA-seq数据的工具性能,与正交的m6A数据集进行比较.
主要成果:
- 在不同数据集和物种中观察到工具性能的显著差异.
- m6A检测工具基于其基本方法表现出明显的精确召回权衡.
- 工具精度和回忆受测序深度的影响,这表明增加测序的好处.
- 调整度切线允许用户调整精密召回平衡.
结论:
- NanOlympicsMod为m6A检测工具的标准化基准测试提供了一个强大的平台.
- 该管道有助于对各种dRNA-seq数据的工具进行比较,有助于选择合适的方法.
- 未来纳米奥运会Mod中新型工具的纳入将增强RNA修饰的表征和发现.
相关概念视频
03:21RNA-seq
10.0K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
02:24Ribosome 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...
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...
3.5K