Simultaneous sequencing of the genome and transcriptome at the single-cell level is a powerful tool for characterizing genomic and transcriptomic variation and revealing correlative relationships. However, it remains technically challenging to analyze both the genome and transcriptome in the same cell. Here, we report a novel method for simultaneous isolation of genomic DNA and total RNA (SIDR) from single cells, achieving high recovery rates with minimal cross-contamination, as is crucial for accurate description and integration of the single-cell genome and transcriptome. For reliable and efficient separation of genomic DNA and total RNA from single cells, the method uses hypotonic lysis to preserve nuclear lamina integrity and subsequently captures the cell lysate using antibody-conjugated magnetic microbeads. Evaluating the performance of this method using real-time PCR demonstrated that it efficiently recovered genomic DNA and total RNA. Thorough data quality assessments showed that DNA and RNA simultaneously fractionated by the SIDR method were suitable for genome and transcriptome sequencing analysis at the single-cell level. The integration of single-cell genome and transcriptome sequencing by SIDR (SIDR-seq) showed that genetic alterations, such as copy-number and single-nucleotide variations, were more accurately captured by single-cell SIDR-seq compared with conventional single-cell RNA-seq, although copy-number variations positively correlated with the corresponding gene expression levels. These results suggest that SIDR-seq is potentially a powerful tool to reveal genetic heterogeneity and phenotypic information inferred from gene expression patterns at the single-cell level.

在单细胞水平上对基因组和转录组同时进行测序是表征基因组和转录组变异并揭示相关关系的强大工具。然而，分析同一细胞中的基因组和转录组在技术上仍然具有挑战性。在这里，我们报告了一种从单细胞同时分离基因组DNA和总RNA（SIDR）的新方法，以最小的交叉污染实现了高回收率，这对于准确描述和整合单细胞基因组和转录组至关重要。为了可靠，有效地从单个细胞中分离基因组DNA和总RNA，该方法使用低渗裂解来保留核层完整性，随后使用偶联抗体的磁微珠捕获细胞裂解液。使用实时PCR评估该方法的性能证明，该方法可有效回收基因组DNA和总RNA。全面的数据质量评估表明，通过SIDR方法同时分离的DNA和RNA适用于单细胞水平的基因组和转录组测序分析。通过SIDR（SIDR-seq）对单细胞基因组和转录组测序的整合显示，与常规单细胞相比，单细胞SIDR-seq更准确地捕获了遗传改变，例如拷贝数和单核苷酸变异RNA-seq，尽管拷贝数变异与相应的基因表达水平正相关。