Sample multiplexed scRNA-seq using Nanocoding method for sample barcode labeling

Sample multiplexed scRNA-seq is a promising strategy to overcome current barriers in high cost and potential technical variations by multiple scRNA-seq tests. In this study, we developed a highly efficienct novel sample barcode labeling method using DNA-encoded Lipid Nanoparticles ('Nanocoding') that could label cells with minimal dependence on their type or sample conditions. This method provids a roubust and general protocol for sample barcoding and multiplexing in scRNA-seq. We demonstrated the performance of Nanocoding through three scRNA-seq studies, which include: 1. mouse spleen cells mix (one dataset including 6 mouse spleen tissues samples); 2. HeLa-mouse Stromal Vascular Fraction(SVF) cells mix (one dataset containing mixed HeLa cell and SVF cell); 3. Aged-Young SVF cells mix (one dataset containing two SVF samples) tests. These studies showcased the biomodal distribution of barcode counts in different models with high signal-to-background ratio, as well as pan-cell labeling activity for efficient and accurate sample-multiplexing. By using Nanocoding, we profiled obsity and age related change in lipid metabolism associated genes or inflammatory related features, in various cell types from spleen or adipose tissues. Male C57BL/6J Diet-Induced-Obese (DIO, N=3) and age-matched C57BL/6J control lean mice (8 month old, N=3) were used for speen collection and following multiplexed scRNA-seq. Each sample is labeled with a unique sample barcode using Nanocoding before mixing. Male C57BL/6J DIO mice that are 8 month old are used for visceral adipose tissue (VAT) collections and SVF cell collection in HeLa-SVF cell mixing test. Male C57BL/6J DIO mice that are 11 month old (N=3) or 4 month old (N=3) are used for visceral adipose tissue (VAT) collections and SVF cell collation in Young-Aged SVF cell mix test.