Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

• DOI: 10.1038/s41467-017-02659-x
• Publication Date: 2018-02-19T11:43:27Z
• Authors: William Stephenson; Laura T. Donlin; Andrew Butler; Cristina Rozo; Bernadette Bracken; Ali Rashidfarrokhi; Susan M. Goodman; Lionel B. Ivashkiv; Vivian P. Bykerk; Dana E. Orange; Robert B. Darnell; Harold P. Swerdlow; Rahul Satija
• Keywords: Single-Cell Analysis; Profiling (computer programming)

Droplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While this approach offers the exciting promise to deconvolute heterogeneity in diseased tissues, lack of cost-effective and user-friendly instrumentation hindered widespread adoption droplet microfluidic techniques. To address this, we developed 3D-printed, low-cost control instrument deploy it clinical environment perform transcriptome profiling disaggregated synovial tissue from five rheumatoid arthritis patients. We sequence 20,387 single cells revealing 13 transcriptomically distinct clusters. These encompass an unsupervised draft atlas autoimmune infiltrate that contribute disease biology. Additionally, identify previously uncharacterized fibroblast subpopulations discern their spatial location within synovium. envision will have broad utility both research settings, enabling routine application