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对于单细胞CRISPR/Cas9谱系追踪条形码数据的贝叶斯系动力学推理框架,其中有依赖的目标站点

A Zwaans^1,2, S Seidel^1,2, M Manceau^1,2

¹Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

|February 20, 2025

概括

我们使用贝叶斯推理 (GABI) 开发了GESTALT分析,从基于CRISPR的动态谱系追踪数据中重建细胞谱系树. 该方法提供了对发育生长动态的可靠估计,这对于理解生物体发育至关重要.

科学领域:

发展生物学发展生物学
计算生物学计算生物学
基因组学就是基因组学.

背景情况:

了解单细胞血统关系是破译发育细胞动态的关键.
基于CRISPR的动态谱系追踪使用基因组编辑来创建用于重建细胞谱系树 (家族遗传树) 的遗传条码.
以前的计算策略已经从谱系追踪数据中改进了树木估计.

研究的目的:

引入使用贝叶斯推理 (GABI) 的GESTALT分析,使用合成目标数组的基因组编辑用于谱系追踪 (GESTALT) 数据进行基因推理的框架.
为了能够在绝对时间中表示树不确定性和缩放.
量化发育过程,如生长,分化和亡,使用植物动力学推理.

主要方法:

将GESTALT数据分析集成到BEAST 2软件中,使用贝叶斯推理.
应用出生-死亡或凝聚模型在时间尺度的血统树上进行植物动力学推断.
验证GABI方法论关于早期*Danio rerio*发展的验证.

主要成果:

GABI为谱系追踪数据提供了一个完全集成的贝叶斯系遗传推断框架.
该方法允许在重建的细胞系谱树中对不确定性的可靠估计.
时间尺度的血统树使得可以对早期 *Danio rerio* 发育中的生长动态进行可靠的量化.

结论:

GABI提供了一种强大的工具,可以对基于CRISPR的血统追踪数据进行强大的家族遗传推断和家族动力学分析.
开发的方法准确地估计了发展增长动态.
GABI代码库是公开可用的,用于更广泛的科学用途.

关键词:

野兽2 在线观看克里斯普尔是什么意思?克里斯普尔是什么意思?丹尼奥·雷里奥 (Danio Rerio) 是一个谱系追踪谱系追踪谱系追踪植物动力学学.一个单细胞的单细胞.

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