inDrops-2: a flexible, versatile and high-throughput single-cell RNA-seq method

Herein, we introduce inDrops-2, an open-source platform for single-cell RNA sequencing (scRNA-seq) tailored for profiling both freshly obtained and preserved clinical samples. This platform exhibits a sensitivity comparable to cutting-edge commercial systems but at a substantially reduced cost. Using inDrops-2, we conducted a comparative analysis of two prominent scRNA-seq protocols those based on template switching and in vitro transcription – and provide new insights about the technical biases inherited to each approach.