Rxivist logo

Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic Instrumentation

By William Stephenson, Laura T. Donlin, Andrew Butler, Cristina Rozo, Ali Rashidfarrokhi, Susan M. Goodman, Lionel B. Ivashkiv, Vivian P. Bykerk, DE Orange, Robert B. Darnell, Harold P. Swerdlow, Rahul Satija

Posted 22 May 2017
bioRxiv DOI: 10.1101/140848 (published DOI: 10.1038/s41467-017-02659-x)

Droplet-based single cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While these approaches offer the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective, reliable, and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we have developed a microfluidic control instrument that can be easily assembled from 3D printed parts and commercially available components costing approximately $540. We adapted this instrument for massively parallel scRNA-seq and deployed it in a clinical environment to perform single cell transcriptome profiling of disaggregated synovial tissue from a rheumatoid arthritis patient. We sequenced 8,716 single cells from a synovectomy, revealing 16 transcriptomically distinct clusters. These encompass a comprehensive and unbiased characterization of the autoimmune infiltrate, including inflammatory T and NK subsets that contribute to disease biology. Additionally, we identified fibroblast subpopulations that are demarcated via THY1 (CD90) and CD55 expression. Further experiments confirm that these represent synovial fibroblasts residing within the synovial intimal lining and subintimal lining, respectively, each under the influence of differing microenvironments. We envision that this instrument will have broad utility in basic and clinical settings, enabling low-cost and routine application of microfluidic techniques, and in particular single-cell transcriptome profiling.

Download data

  • Downloaded 4,166 times
  • Download rankings, all-time:
    • Site-wide: 1,144 out of 100,263
    • In genomics: 235 out of 6,218
  • Year to date:
    • Site-wide: 35,315 out of 100,263
  • Since beginning of last month:
    • Site-wide: None out of 100,263

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News

  • 20 Oct 2020: Support for sorting preprints using Twitter activity has been removed, at least temporarily, until a new source of social media activity data becomes available.
  • 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
  • 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
  • 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
  • 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
  • 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
  • 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
  • 22 Jan 2019: Nature just published an article about Rxivist and our data.
  • 13 Jan 2019: The Rxivist preprint is live!