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单细胞基因组学研究中的时间相关伪影采样。

Sampling time-dependent artifacts in single-cell genomics studies.

机构信息

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.

Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, Spain.

出版信息

Genome Biol. 2020 May 11;21(1):112. doi: 10.1186/s13059-020-02032-0.

DOI:10.1186/s13059-020-02032-0
PMID:32393363
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7212672/
Abstract

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention.

摘要

强大的方案和自动化技术如今已能实现大规模单细胞 RNA 和 ATAC 测序实验及其在生物库和临床队列中的应用。然而，在样本采集过程中引入的技术偏差可能会阻碍可靠、可重复的结果，因此在进入大规模数据生产之前，需要进行系统的基准测试。在这里，我们报告了在采样过程中引入的基因表达和染色质可及性伪影的存在和程度，并确定了预防这些伪影的实验和计算解决方案。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c41/7212672/34b1851a84c0/13059_2020_2032_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c41/7212672/41e40d9c0970/13059_2020_2032_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c41/7212672/34b1851a84c0/13059_2020_2032_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c41/7212672/41e40d9c0970/13059_2020_2032_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9c41/7212672/34b1851a84c0/13059_2020_2032_Fig2_HTML.jpg

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