Advantages of single nucleus over single cell RNA-seq in adult kidney

A key limitation in single cell genomics is generating a high-quality single cell suspension that contains rare or difficult to dissociate cell types and is free of RNA degradation or transcriptional stress responses. Samples with unpredictable availability or that must be collected at several timepoints present additional challenges. Using adult mouse kidney, we compared single-cell RNA sequencing (scRNA-seq) data generated using DropSeq with snRNA-seq data generated from nuclei using sNuc-DropSeq, DroNc-seq and 10X Chromium. We validated snRNA-seq on fibrotic kidney from day 14 unilateral ureteral obstruction (UUO). Dropseq, sNucDropseq, DroNcSeq and 10X Chromium were used to profile mouse healthy and fibrotic kidneys单细胞基因组学领域的一项关键局限，在于如何制备同时包含稀有或难解离细胞类型、且无RNA降解或转录应激反应的高质量单细胞悬液。可获取性难以预判，或需在多个时间点采集的样本，更会增添额外实验挑战。本研究以成年小鼠肾脏为研究对象，对比了采用DropSeq技术生成的单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据，与使用sNuc-DropSeq、DroNc-seq及10X Chromium技术从细胞核中获取的单细胞核RNA测序（single-nucleus RNA sequencing, snRNA-seq）数据。此外，我们针对造模后第14天的单侧输尿管梗阻（unilateral ureteral obstruction, UUO）纤维化肾脏样本，对snRNA-seq技术开展了验证实验。本研究使用Dropseq、sNucDropseq、DroNcSeq及10X Chromium技术，完成了小鼠健康肾脏与纤维化肾脏的组学表征分析。