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通过cDNA分子匹配进行单细胞长读和短读转录组测序的比较:MAS-ISO-seq方法的质量评估

Natalia Zajac^1,2, Qin Zhang¹, Anna Bratus-Neuenschwander¹

¹Functional Genomics Center Zurich, ETH Zurich and University of Zurich, 8057 Zurich, Switzerland.

NAR genomics and bioinformatics

|July 9, 2025

概括

短读和长读单细胞RNA测序方法产生可比的基因表达数据. 然而,偏差来自图书馆准备和生物信息处理,影响着转录恢复和基因计数相关性.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

单细胞RNA测序 (scRNA-seq) 对于理解细胞异质性至关重要.
短读序列提供高吞吐量,而长读序列提供异形分辨率.
短读和长读scRNA-seq数据之间的可比性和偏差仍然不清楚.

研究的目的:

调查图书馆准备和生物信息学中的偏见,用于短读和长读scRNA-seq.
评估过全长转录对基因表达的影响.
为了比较Illumina短读和太平洋生物科学长读之间的数据可比性.

主要方法:

使用Illumina短读数和PacBio长读数对相同的10x Genomics 3'cDNA样本进行了测序.
使用细胞条形码和独特的分子标识符进行交叉比较.
分析了在图书馆准备和生物信息处理过程中引入的偏差.

主要成果:

无论是短读还是长读的方法都能恢复很大比例的细胞和高可比性的转录.
在cDNA库处理和数据分析中观察到平台特定的偏差.
长读序列更好地保留短转录 (<500 bp) 并删除退化的cDNA.
过文物,只能在全长的转录中识别,基因数量下降的相关性.

结论:

短读和长读scRNA-seq在很大程度上是可比的,但引入了不同的偏差.
从长时间读取的全长转录信息可以删除文物,提高数据质量.
仔细考虑图书馆准备和生物信息管道对于准确的scRNA-seq分析至关重要.

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