Automating single-cell RNA-sequencing (scRNA-seq) protocols on robotic platforms has the potential to enable unbiased, transcriptomic analyzes of individual cells at an unprecedented scale. Liquid handling steps for scRNA-seq on robotic platforms must be accurate and robust to avoid any loss of material, prevent cross-contamination and limit the introduction of technical error into sequencing data. Furthermore, miniaturization of sample preparation results in a significantly reduced cost-per-cell that is essential for large-scale single-cell studies. Here we present the use of TTP Labtech mosquito® liquid handlers to automate and miniaturize two very different scRNA-seq protocols, CEL-Seq2 and SMARTer-Seq. The mosquito liquid handler is a versatile and easy-to-use platform that is capable of a broad-range of liquid-handling functions, including both dispensing and aspiration. Semi-automatedmagnetic bead purification at low volume is also facilitated on the system. This setup allows for highthroughput, parallel processing of single cells on 384-
well plates, providing a significant reduction in reaction volume and hands-on time, while maintaining or improving data quality compared with manual liquid-handling.