A Dataset Examining Technical Factors on Fixed Whole Blood Single-Cell RNA-Seq

High-throughput sequencing technologies have enabled many biological discoveries; nevertheless, the resolution of bulk RNA sequencing is insufficient to elucidate the heterogeneity at the single-cell level. Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for disentangling this complexity.. A major challenge in scRNA-Seq of blood is the analysis of granulocytes. These cells are pivotal to immunological responses but are recalcitrant to isolation from blood without inducing activation artifacts, thereby perturbing their transcriptomic integrity.. The difficulty of granulocyte handling for scRNA-Seq necessitate immediate processing of samples, a workflow incompatible with the logistical demands of large-scale, multi-centric studies. Innovations in commercial fixed scRNA-Seq methodologies promise to ameliorate these limitations by preserving RNA integrity post-fixation. Our investigation evaluates two such commercial kits for fixed scRNA-Seq. Our overall goal was to determine feasibility for distributed collection and centralised processing of fixed whole blood samples. The dataset consists of 2 technology platforms; Honeycomb HIVE v1 and 10x Genomics Flex v1. This consists of 2 batches of HIVE and 4 batches for 10x Genomics. In total there are 18 samples; 2 for HIVE and 16 for Flex. The underlying samples are red blood cell depleted whole blood from healthy donors (Figure 1). For 10x Genomics Flex batch 3, we received a replacement set of library preparation reagents due to poor performance of this batch “batch 3A”. As instructed by 10x Genomics field application specialist we performed a second capture reaction of remaining material from batch 3A = “batch 3B”.