Split-pool combinatorial barcoding sequencing of murine immune cells

Single-cell RNA sequencing experiments commonly use 10x Genomics kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. The Parse technology allows the analysis of more cells from multiple samples in a single run without using additional reagents or specialized microfluidics equipment. To assess the efficacy of both platforms, we carried out a benchmark study using biological and technical replicates of young murine thymus as a complex immune tissue. To optimally utilize the capacity of Parse high-throughput kits, we also performed sequencing of murine splenocytes from a chronic stress model and control animals. Thymic and splenic samples from young and adult mice (20 in total) were extracted and pooled together to run on a single Parse WT kit. The resulting Parse library was split into nine sublibraries (PWT_1-PWT_9). Thymocytes from separate biological replicates were processed with the Parse Mini kit and split into two sublibraries. The 10x Genomics data contains thymocytes from two biological and two technical replicates multiplexed using cell hashing technology.