Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.
Genome Biol. 2024 Mar 22;25(1):78. doi: 10.1186/s13059-023-03150-1.
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16) model. Our study of CC16 nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.
我们开发了一种大规模的单细胞 ATAC-seq 方法，将基于 Tn5 的预索引与 10× Genomics 条形码技术相结合，可在单个反应中对多达 200000 个核进行索引。我们对包括人皮质、鼠脑、人肺、鼠肺、鼠肝和 CC16 模型的肺泡Ⅱ型细胞蛋白敲除鼠肺组织在内的多种组织中的 449953 个核进行了分析。我们对 CC16 核的研究揭示了以前未被充分认识的技术伪影，这些伪影源于残留的 129 鼠种遗传物质，它们导致许多基因附近的调控元件发生深刻的细胞类型特异性变化，从而混淆了对这个常用参考鼠模型的解释。
