Single-cell technologies are becoming increasingly widespread and have been revolutionizing our understanding of cell identity, state, diversity and function. Unravelling the complexity of embryonic development and disease at the single-cell level is a fascinating goal of humankind. However, current single-cell technologies can be slow to apply to large-scale studies and resource-limited clinical arenas due to a variety of reasons including cost, infrastructure, sample quality and requirements. We developed DNBelab C4 (C4), a negative pressure orchestrated, portable and cost-effective device that enables high-throughput single-cell transcriptional and epigenetic profiling. C4 system can efficiently allow discrimination of species-specific cells at high resolution and dissect tissue heterogeneity in different organs, and has huge benefits in cost and portability. We applied this system to large-scale profiling of transcriptome and chromatin accessibility landscapes of a non-human primate, cynomolgus monkey (Macaca fascicularis), to understand the distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes. We found substantial heterogeneity of ACE2 expression across the lung, kidney, thyroid and liver. We identified a potential link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding SARS-CoV-2 pathophysiology, which might guide in the development of effective treatments and preventative strategies of COVID-19.