Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (12): 109-117.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0518
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ZHAO Ruo-han(), ZHAO Jing-ying, BAI Yi-cheng, ZHANG Rui-fang, JIA Jun-jing, DOU Teng-fei()
Received:
2023-05-31
Online:
2023-12-26
Published:
2024-01-11
Contact:
DOU Teng-fei
E-mail:1027261505@qq.com;tengfeidou@sina.com
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.
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
Table 1 Introduction to seven scATAC-seq technologies
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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。 | [ |
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