MAPS-seq: magnetic bead-assisted parallel single-cell gene expression profiling

Recently developed single-cell RNA sequencing methods allow the simultaneous profiling of the transcriptomes of thousands of individual cells. However, current methods still require advanced equipment or entail substantial waste of reagents. Here, we introduce magnetic bead-assisted parallel single-cell gene expression sequencing (MAPS-seq), a microwell-based method that pools samples before the reverse transcription step, increasing the ease of sample preparation and reducing reagent waste. Moreover, because this method uses universal reagents and standard molecular biology lab instruments, it is easy to implement, even in labs that have not previously conducted single-cell RNA sequencing. We validated our method by demonstrating that it can generate gene expression data at the single-cell level. We then applied the MAPS-seq method to analyze 237 human myelogenous leukemia cells treated with one of three different drugs or dimethyl sulfoxide. We observed transcriptional changes and identified marker genes that indicate a drug response. Furthermore, the MAPS-seq method produced data of comparable quality to those of existing single-cell RNA sequencing methods. Consequently, we expect that our method will provide researchers with a more accessible, less wasteful, and less burdensome method for investigating the transcriptomes of individual cells.