Linked optical and gene expression profiling of single cells at high throughput

Single cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through gene expression alone. Linking sequencing with optical analysis has provided insight into the molecular basis behind cellular function, but current approaches have limited throughput. Here, we present a high throughput platform for linked optical and gene expression profiling of single cells. We demonstrate accurate fluorescence and gene expression measurements from thousands of cells in a single experiment and use the platform to characterize DNA and RNA changes in Jurkat cells through the cell-cycle. In addition to its scalability, our integration of microfluidics and array-based molecular biology holds promise for comprehensive multi-omics profiling of single cells. Overall design: Linked flow cytometry and gene expression datasets from mouse and human cells stained with red and green live cell dyes, Jurkat cells stained with a DNA-binding dye, and PBMCs labeled with antibodies against CD14 and CD16.