A diffusion-based microfluidic device for single-cell RNA-seq

Microfluidic devices provide a low-input and efficient platform for single-cell RNA-seq (scRNA-Seq). Here we present microfluidic diffusion-based RNA-seq (MID-RNA-seq) for conducting scRNA-seq with a diffusion-based reagent swapping scheme. This device incorporates cell trapping, lysis, reverse transcription and PCR amplification all in one microfluidic chamber. MID-RNA-Seq provides high data quality that is comparable to existing scRNA-seq methods while implementing a simple device design that permits multiplexing. The robustness and scalability of MID-RNA-Seq device will be important for transcriptomic studies of scarce cell samples. Overall design: We performed single-cell RNA-seq from human and mouse cell lines using MID-RNA-seq devices. We produced 6 scRNA-seq data sets using single GM12878 cells and 6 data sets using single MEF cells using three 2-unit devices in each case. We also generated 4 data sets using a 4-unit MID-RNA-Seq device using 10 pg RNA in each unit. In addition, we produced 29 data sets on single GM12878 cells in 5 runs of the 6-unit device. Furthermore, 2 bulk RNA-seq samples using 1000 cells each were prepared using a commercial kit. In the file names, "SC" indicates single cell RNA-seq data set, followed by cell line name (either "GM12878" or "MEF"), the type and number of device used (e.g. "2UnitDevice1" or "6UnitDevice1"), and the number of the unit with a multi-unit device (e.g. "U1" or "U2").