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DIRECT: Digital Microfluidics for Isolation-Free Shared Library Construction of Single-Cell DNA Methylome and Transcriptome

ABSTRACT: Integrated single-cell transcriptome and DNA methylome profiling has provided insight into the complex regulatory networks of cells. Existing methods are based on picking a single-cell and performing library construction in a tube, which is costly and cumbersome. Here, we propose DIRECT, a digital microfluidics-based method for simultaneous analysis of the methylome and transcriptome in a single library construction. The accuracy of DIRECT is demonstrated in comparison with bulk and single-omics data, and the high CpG site coverage of DIRECT allows for precise analysis of copy number variation information, enabling expansion of single cell analysis from two- to three-omics. By applying DIRECT to monitor the dynamics of mouse embryonic stem cell differentiation, the relationship between DNA methylation and changes in gene expression during differentiation was revealed. DIRECT enables accurate, robust, and reproducible single-cell DNA methylation and gene expression co-analysis at a lower cost and with greater efficiency, broadening the application scenarios of single-cell multi-omics analysis and revealing a more comprehensive and fine-grained map of cellular regulatory landscapes.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE240579 | GEO | 2023/08/10

REPOSITORIES: GEO

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