Single Cell Assay for Transposase Accessible Chromatin with High-throughput Sequencing Technology and Its Applications

doi:10.13560/j.cnki.biotech.bull.1985.2023-0518

Abstract

Abstract:

Single-cell assay for transposase-accessible chromatin with high-throughput sequencing（scATAC-seq）is a high-throughput sequencing technique that utilizes transposase to investigate the chromatin accessibility at the single-cell level, which is of great significance for investigating the epigenetic regulation of the whole genome. It can reveal important information about chromatin organization from multiple perspectives, mapping the binding regions of transcription factors and the positioning of nucleosomes in cells. Currently, scATAC-seq has been widely applied in the fields of biology and medicine, primarily for generating open chromatin profiles, studying cell differentiation and development, elucidating disease pathogenesis, and exploring the tumor microenvironment. This article provides an overview of the development, data analysis, and relevant applications of scATAC-seq technology in studying the open chromatin regions at the single-cell level, aiming to provide insights for the investigation of chromatin accessibility at the single-cell whole-genome level, identification of cis-regulatory elements, and deciphering genetic regulatory networks, thereby contributing to advancements in life science research.

Key words: scATAC-seq, data analysis, application

ZHAO Ruo-han, ZHAO Jing-ying, BAI Yi-cheng, ZHANG Rui-fang, JIA Jun-jing, DOU Teng-fei. Single Cell Assay for Transposase Accessible Chromatin with High-throughput Sequencing Technology and Its Applications[J]. Biotechnology Bulletin, 2023, 39(12): 109-117.

Figures/Tables 3

References 50

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技术 Technology	检测的细胞数量 Number of detected cells	细胞类型 Cell type	目的 Objective	特点 Characteristic	参考文献 Reference
sci-ATAC	1 500个左右	任何细胞类型	获取染色质可及性信息	1.方法简单易行，适用于实验室； 2.测序覆盖范围相对较低； 3.随着板数量的增加，测序成本增加； 4.该技术尚未实现商业化，在实际操作中缺乏客观有效的操作流程，通常需要针对不同批次进行定制和微调。	[6,12]
Fluidigm C1	一次上样的细胞数为96个	直径在5-25 μm的细胞	获取染色质可及性信息	1.稳定的细胞捕获平台； 2.对操作者的技术要求较低； 3.实验周期短； 4.细胞通量低； 5.成本较高。	[13]
scTHS	60 000个	新鲜或冻存的组织样本	获取染色质可及性信息和提高了远端增强子信息	1.检测染色质可及性具有高灵敏度和特异性； 2.捕获转录起始位点附近和远端调控区域的较小峰值方面具有优势； 3.需定制Tn5转座酶； 4.对操作人员的技术要求较高； 5.成本相对较高。	[14]
uATAC	一次可以分离1 800个单细胞	适用于5-100 μm范围的活细胞	获取染色质可及性信息	1.实现无细胞大小偏好的分选； 2.单细胞反应孔可视化； 3.可筛选活的单细胞进行后续处理，可节约反应试剂并缩短数据分析时间； 4.细胞捕获效率低。	[15]
Plate	5 000-50 000个细胞	新鲜或冷冻保存的纯细胞	获取染色质可及性信息	1.无需昂贵的设备； 2.成本较低； 3.适用于分离培养的细胞； 4.细胞通量低。	[16]
dsci-ATAC	100 000个细胞	新鲜的组织样本	获取染色质可及性信息	1.该技术解决了快速分离细胞的挑战，显著提高了单细胞分析的速度； 2.细胞通量高； 3.高灵敏度； 4.成本相对较高。	[17]
10X	每次可处理8个样本，细胞通量高达80 000个以上	直径40 μm以下的活细胞	获取染色质可及性信息	1.操作流程自动化程度高； 2.细胞捕获效率高； 3.对细胞总量及活性要求较高，需仪器上门服务； 4.成本相对较低。	[9]

技术 Technology	检测的细胞数量 Number of detected cells	细胞类型 Cell type	目的 Objective	特点 Characteristic	参考文献 Reference
sci-ATAC	1 500个左右	任何细胞类型	获取染色质可及性信息	1.方法简单易行，适用于实验室； 2.测序覆盖范围相对较低； 3.随着板数量的增加，测序成本增加； 4.该技术尚未实现商业化，在实际操作中缺乏客观有效的操作流程，通常需要针对不同批次进行定制和微调。	[6,12]
Fluidigm C1	一次上样的细胞数为96个	直径在5-25 μm的细胞	获取染色质可及性信息	1.稳定的细胞捕获平台； 2.对操作者的技术要求较低； 3.实验周期短； 4.细胞通量低； 5.成本较高。	[13]
scTHS	60 000个	新鲜或冻存的组织样本	获取染色质可及性信息和提高了远端增强子信息	1.检测染色质可及性具有高灵敏度和特异性； 2.捕获转录起始位点附近和远端调控区域的较小峰值方面具有优势； 3.需定制Tn5转座酶； 4.对操作人员的技术要求较高； 5.成本相对较高。	[14]
uATAC	一次可以分离1 800个单细胞	适用于5-100 μm范围的活细胞	获取染色质可及性信息	1.实现无细胞大小偏好的分选； 2.单细胞反应孔可视化； 3.可筛选活的单细胞进行后续处理，可节约反应试剂并缩短数据分析时间； 4.细胞捕获效率低。	[15]
Plate	5 000-50 000个细胞	新鲜或冷冻保存的纯细胞	获取染色质可及性信息	1.无需昂贵的设备； 2.成本较低； 3.适用于分离培养的细胞； 4.细胞通量低。	[16]
dsci-ATAC	100 000个细胞	新鲜的组织样本	获取染色质可及性信息	1.该技术解决了快速分离细胞的挑战，显著提高了单细胞分析的速度； 2.细胞通量高； 3.高灵敏度； 4.成本相对较高。	[17]
10X	每次可处理8个样本，细胞通量高达80 000个以上	直径40 μm以下的活细胞	获取染色质可及性信息	1.操作流程自动化程度高； 2.细胞捕获效率高； 3.对细胞总量及活性要求较高，需仪器上门服务； 4.成本相对较低。	[9]