单细胞和空间替代拼接分析使用纳米孔长读数测序
Yuntian Fu1, Heonseok Kim2,3,4,5, Sharmili Roy2
1Graduate Program in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. yuntianf@pennmedicine.upenn.edu.
Nature communications
|July 19, 2025
概括
长细胞通过改进异形量化和分析拼接变异来增强单细胞和空间转录组学的长读序列. 这个计算管道克服了纳米孔测序的挑战,揭示了对基因表达的新见解.
科学领域:
- 单细胞基因组学 单细胞基因组学
- 空间转录组学 空间转录组学
- 计算生物学是一种计算生物学.
- 分析RNA序列的分析.
背景情况:
- 长读测序为替代拼接分析提供了优势,但在单细胞和空间应用中面临技术障碍.
- 纳米孔测序中的高错误率会影响细胞条形码和UMI恢复,而读取截断和错位会影响异形量化.
- 缺乏强大的统计框架阻碍了在单个细胞或空间位置内和单个细胞或空间位置之间对拼接变化的评估.
研究的目的:
- 介绍 Longcell,一个计算管道,旨在从单细胞和空间条形码的 Nanopore 来进行异形量化. 长读.
- 解决复杂生物样本中长期读取的测序数据的替代拼接分析的技术和计算障碍.
- 为了能够在单细胞和空间层面上统计评估拼接变异.
主要方法:
- 开发一个统计和计算管道 (Longcell) 处理纳米孔长读数据.
- 实施算法,以有效地恢复细胞条形码和UMI (独特分子标识符).
- 纳米孔读取错误纠正方法的集成和拼接多样性的建模.
- 将Longcell应用于多个数据集,包括针对拼接因子的扰动实验.
主要成果:
- 长细胞成功地恢复了细胞条形码和UMI,纠正了测序错误,并从单细胞和空间长读数据中量化了异型.
- 管道准确地识别了不同数据集的空间异形切换事件.
- 分析显示,高度表达的基因具有广泛的高细胞内异构异质性.
- 扰乱实验确定了拼接因子的监管目标,通过有针对性的测序来验证.
结论:
- 长细胞提供了一个强大的解决方案,用于单细胞和空间环境中使用纳米孔长读序列的异形量化和拼接变异分析.
- 这些发现强调了Longcell在揭示复杂的拼接动态和监管关系方面的实用性.
- 这项工作促进了长期阅读测序技术在转录学研究中的应用.
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