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基因表达:从单细胞RNA测序数据集的基因表达基于记忆的血统推断.

A S Eisele1, D M Suter2

  • 1Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland. almut.eisele@epfl.ch.

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概括

基因表达基于记忆的谱系推断 (GEMLI) 从单细胞RNA测序数据预测细胞谱系. 这种计算工具分析基因表达模式,以在没有物理分离的情况下追踪细胞发育,从而简化了谱系注释.

关键词:
细胞家族是一个细胞家族.克隆性 克隆性是指克隆性决定命运的决定基因表达记忆 基因表达记忆基因表达稳定性 基因表达稳定性血统推断推断的结论是谱系追踪 谱系追踪 谱系追踪记忆基因 记忆基因是记忆的基因.单调地表达的基因多细胞结构是多细胞结构.

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科学领域:

  • 计算生物学 计算生物学
  • 基因组学就是基因组学.
  • 发展生物学 发展生物学

背景情况:

  • 传统的血统追踪方法依赖于遗传标记或物理细胞分离.
  • 单细胞RNA测序 (scRNA-seq) 提供了一种高通量方法来研究细胞异质性.
  • 从scRNA-seq数据中预测细胞系对于理解发育和疾病至关重要.

研究的目的:

  • 介绍并详细介绍基因表达基于记忆的谱系推断 (GEMLI) R包的使用情况.
  • 为了证明GEMLI如何使用scRNA-seq数据的基因表达记忆来预测细胞系.
  • 为分析基因谱系信息提供一个协议,包括基因表达记忆和细胞命运决定.

主要方法:

  • GEMLI利用基因表达记忆的原理,其中基因表达水平通过细胞分裂得到维持.
  • 该研究提供了使用GEMLI R包在scRNA-seq基因表达矩阵上的详细协议.
  • 方法包括参数调整,谱系信息提取,可视化和微调.

主要成果:

  • GEMLI仅从scRNA-seq数据进行血统预测,远离实验方法.
  • 该工具有助于研究细胞系在发育,平衡,再生和疾病中的研究.
  • GEMLI可以剖析细胞类型特定的基因表达记忆,区分细胞命运决策,并重建多细胞结构.

结论:

  • GEMLI提供了一种强大的计算方法来推断细胞系,大大简化和扩展系谱注释.
  • 该R包是多功能,适用于各种生物环境和scRNA-seq数据类型.
  • 在人类样本中识别小系谱时,GEMLI特别有希望,在其他方法不适用的情况下.