单细胞DNA甲基化测序数据处理流程与分析方法

doi:10.16288/j.yczz.24-154

遗传 ›› 2024, Vol. 46 ›› Issue (10): 807-819.doi: 10.16288/j.yczz.24-154

单细胞DNA甲基化测序数据处理流程与分析方法

王艳妮¹(), 李佳¹^,²^,³()

1.广州实验室，广州 510200
2.广州医科大学，呼吸疾病全国重点实验室，广州 510200
3.广州医科大学附属肿瘤医院，肿瘤研究所，广州 510200

收稿日期:2024-05-30 修回日期:2024-08-30 出版日期:2024-09-12 发布日期:2024-09-12
通讯作者: 李佳，博士，教授，研究方向：表观遗传学。E-mail: li_jia@gzlab.ac.cn
作者简介:王艳妮，硕士研究生，专业方向：遗传学。E-mail: wang_yanni@gzlab.ac.cn
基金资助:
国家自然科学基金项目(82370148);农村和社会发展科技处/广州医科大学/广州医科大学附属第一医院重点研发计划(2024B03J0046);广州国家实验室专项项目(GZNL2023A02003);呼吸疾病国家重点实验室自主开放课题项目(J19112006202302);广州医科大学/附属肿瘤医院科研能力提升项目(02-410-2302244XM);呼吸疾病全国重点实验室自主课题基金(SKLRD-Z-202307)

Processing pipelines and analytical methods for single-cell DNA methylation sequencing data

Yanni Wang¹(), Jia Li¹^,²^,³()

1. Guangzhou Laboratory, Guangzhou 510200, China
2. State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 510200, China
3. Cancer Research Institute, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou 510200, China

Received:2024-05-30 Revised:2024-08-30 Published:2024-09-12 Online:2024-09-12
Supported by:
National Natural Science Foundation of China(82370148);Rural and Social Development Science and Technology Office/Guangzhou Medical University/Guangzhou Medical University First Affiliated Hospital Key R&D Plan(2024B03J0046);Guangzhou National Laboratory Special Project(GZNL2023A02003);Independent Open Subject Project of the State Key Laboratory of Respiratory Diseases(J19112006202302);Guangzhou Medical University/Affiliated Cancer Hospital Scientific Research Capacity Improvement Project(02-410-2302244XM);Independent Research Fund of the State Key Laboratory of Respiratory Diseases(SKLRD-Z-202307)

摘要/Abstract

摘要：

单细胞DNA甲基化测序技术近年来取得了飞速发展，在揭示细胞间异质性及表观遗传学调控机制方面发挥着重要作用。随着测序技术的进步，单细胞甲基化数据的质量与数量也在不断提高，标准化的预处理流程与合适的分析方法对确保数据的可比性与结果的可靠性尤为关键。然而，目前尚未形成一套完整的数据分析流程来指导研究人员对现有数据进行挖掘。本文系统综述了单细胞甲基化数据预处理步骤和分析方法，简要介绍了相关算法和工具，并探讨了单细胞甲基化技术在脑科学、血细胞分化及癌症研究中的应用前景，旨在为研究人员分析数据时提供指导，推动单细胞甲基化测序技术的发展和应用。

关键词: 单细胞DNA甲基化测序, 表观遗传学, 预处理, 数据分析

Abstract:

Single-cell DNA methylation sequencing technology has seen rapid advancements in recent years, playing a crucial role in uncovering cellular heterogeneity and the mechanisms of epigenetic regulation. As sequencing technologies have progressed, the quality and quantity of single-cell methylation data have also increased, making standardized preprocessing workflows and appropriate analysis methods essential for ensuring data comparability and result reliability. However, a comprehensive data analysis pipeline to guide researchers in mining existing data has yet to be established. This review systematically summarizes the preprocessing steps and analysis methods for single-cell methylation data, introduces relevant algorithms and tools, and explores the application prospects of single-cell methylation technology in neuroscience, hematopoietic differentiation, and cancer research. The aim is to provide guidance for researchers in data analysis and to promote the development and application of single-cell methylation sequencing technology.

Key words: single-cell methylation sequencing, epigenetics, data preprocessing, data analysis

王艳妮, 李佳. 单细胞DNA甲基化测序数据处理流程与分析方法[J]. 遗传, 2024, 46(10): 807-819.

Yanni Wang, Jia Li. Processing pipelines and analytical methods for single-cell DNA methylation sequencing data[J]. Hereditas(Beijing), 2024, 46(10): 807-819.

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技术名称	比对率	一次处理的通量	每个细胞唯一读数数目(测序深度)	CpGs位点	亚硫酸氢盐转化率	优点
Drop-BS	65%	2天10,000细胞	41,013 (231,382)	24,230	99%	短时间可处理大量细胞
snmC-seq	55%	每板384细胞	1.7 M(6.9 M)	1.7 M	99%	-
snmC-seq2	65%	结合机器对6144细胞混合测序	-	-	99%	覆盖均匀
sciMET	60%	每次实验500~700细胞	186,710 (755,529)	162,045	99%	-
sciMET v2	69%	每次实验1000细胞	3.1 M(4.9 M)	2.2 M	99%	成本低
scBS-seq	20%	文章中测序44细胞	3.0 M(19.4 M)	3.7 M	98.5%	测序深度高

去接头工具名	优点	是否支持多线程	来源
Cutadapt	适用范围广，应用较为广泛	是	https://github.com/marcelm/cutadapt
TrimGalore	集成了FastQC的功能，有专门用于RRBS数据的模式	是	https://github.com/FelixKrueger/TrimGalore
Fastp	集成了FastQC和Trimmomatic的功能，处理速度快、内存占用低	是	https://github.com/OpenGene/fastp
Trimmomatic	灵活、高效	是	https://github.com/timflutre/trimmomatic

单细胞DNA甲基化测序数据处理流程与分析方法

Processing pipelines and analytical methods for single-cell DNA methylation sequencing data

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