Dissecting single-cell dynamics leveraging micro/nano electroporation

Abstract

We here introduce approaches, SINC-seq (single-cell integrated nuclear and cytoplasmic RNA-sequencing) and NanoSINC-seq (nanopore-based SINC-seq), that allow us to study the correlated and anti-correlated expressions between cytoplasmic and nuclear transcripts in single cells at unprecedented resolution. We have developed microfluidic approaches that enable fractionation of cytoplasmic versus nuclear RNA in single cells, leveraging microflow and electric field control in a micro/nanometer scale. Our microfluidic approaches electrically and selectively lyse plasma membranes of eukaryotic cells while retaining nuclear membranes relatively intact, electrophoretically extract cytoplasmic components, physically fractionate cytoplasmic versus nuclear molecules and organelle, and automatically output the fractionated sample to individual off-chip analyses within 5 min. We demonstrated the integration of our approaches with off-chip next-generation sequencing to dissect the dynamical processes of post-transcriptional regulation.