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解开基因表达的时间表:对单细胞RNA测序数据的伪时间轨迹分析
Jinming Cheng1,2, Gordon K Smyth1,3, Yunshun Chen1,2,4
1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, 3052, Australia.
F1000Research
|November 23, 2023
概括
本研究介绍了一种R工作流程,用于在小鼠乳腺中进行单细胞RNA测序 (scRNA-seq) 轨迹分析. 它识别了与细胞分化和发育相关的基因,提供了对生物过程的洞察力.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 发展生物学 发展生物学
背景情况:
- 单细胞RNA测序 (scRNA-seq) 能够对单个细胞进行高通量基因表达分析.
- scRNA-seq分析旨在识别细胞亚群,标记基因和发育轨迹.
- 轨迹推断是理解细胞分化和发育过程的关键方法.
研究的目的:
- 展示一个全面的基于R的工作流程,用于对多样本scRNA-seq数据的轨迹推断和时间过程分析.
- 将此工作流应用于小鼠乳腺数据集,以推断细胞分化轨迹.
- 识别与假名时代相关的显著基因,代表发育进展.
主要方法:
- 利用开源的R包来完成一个完整的scRNA-seq分析管道.
- 雇用Seurat进行样本整合和细胞聚类.
- 应用单眼3用于轨迹推断和边缘R用于伪批量时间过程分析.
主要成果:
- 顺序顺序的细胞沿着代表分化和发育的伪时间轨迹.
- 在小鼠乳腺数据集中鉴定出与伪素胺显著相关的基因.
- 证明了轨迹分析对于发现生物过程的有用性.
结论:
- R工作流为scRNA-seq轨迹分析提供了宝贵的资源.
- 轨迹推断对于理解细胞发育和分化是有效的.
- 这种方法可以帮助确定各种生物过程的生物标志物和治疗点.
相关概念视频
03:21RNA-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 microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:24Ribosome Profiling
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 helps...
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 helps...