[RNA-seq] Simultaneous Isolation of DNA-RNA from a single-cell

The simultaneous sequencing of a single cell’s genome and transcriptome is powerful tools to understand the genomic and transcriptomic variations, and their correlative relationships. However, technical obstacles have prohibited the simultaneous analysis of both genome and transcriptome derived from a single cell. Here, we report a method for simultaneous isolation of DNA and total RNA (SIDR) from single cells, especially for parallel genome and transcriptome sequencing. The method adopts a strategy to physically separate genomic DNA and total RNA from single cells, based on hypotonic lysis and subsequent separation of cell lysate associated with magnetic microbeads. Systematic performance evaluation by quantitative real-time PCR and single-cell sequencing demonstrated that the method efficiency recovered genomic DNA and total RNA. We also validated that genomic DNA and total RNA simultaneously fractionated by SIDR method were suitable for the genome and transcriptome sequencing analysis of single cells, based on various aspects of sequencing data quality. By applying SIDR to integrated genome and transcriptome sequencing, this platform may be potentially an enabling tool to merge biological genetic and phenotypic information at the single cell scale.

对单个细胞的基因组（genome）与转录组（transcriptome）进行同步测序，是解析基因组变异、转录组变异及其相关关联的有力研究工具。然而，技术瓶颈此前一直制约了对单个细胞来源的基因组与转录组开展同步分析。本文报道了一种可从单个细胞中同步分离脱氧核糖核酸（deoxyribonucleic acid, DNA）与总RNA的方法（SIDR），尤其适用于并行基因组与转录组测序。该方法基于低渗裂解技术，通过后续结合磁微珠的细胞裂解液分离步骤，实现单个细胞内基因组DNA与总RNA的物理分离。通过实时定量PCR（quantitative real-time PCR）与单细胞测序开展的系统性性能评估结果显示，本方法可高效回收基因组DNA与总RNA。我们还基于测序数据多维度质量指标，验证了经SIDR方法同步分离得到的基因组DNA与总RNA，可满足单个细胞的基因组与转录组测序分析需求。将SIDR方法应用于整合式基因组与转录组测序后，该平台有望成为在单细胞尺度上整合生物学遗传信息与表型信息的实用工具。