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Nat Commun. 2018 Feb 23;9(1):791. doi: 10.1038/s41467-017-02659-x.

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

Author information

1
Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA. wstephenson@nygenome.org.
2
Hospital for Special Surgery, New York, NY, 10021, USA.
3
Weill Cornell Medical College, New York, NY, 10065, USA.
4
New York Genome Center, New York, NY, 10013, USA.
5
New York University, Center for Genomics and Systems Biology, New York, NY, 10003, USA.
6
New York University School of Medicine, New York, NY, 10016, USA.
7
Laboratory of Neuro-Oncology, Rockefeller University, New York, NY, 10065, USA.
8
Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA.
9
Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA.
10
New York Genome Center, New York, NY, 10013, USA. rsatija@nygenome.org.
11
New York University, Center for Genomics and Systems Biology, New York, NY, 10003, USA. rsatija@nygenome.org.

Abstract

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 cellular heterogeneity in diseased tissues, the lack of cost-effective and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we developed a 3D-printed, low-cost droplet microfluidic control instrument and deploy it in a clinical environment to perform single-cell transcriptome profiling of 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 of the autoimmune infiltrate that contribute to disease biology. Additionally, we identify previously uncharacterized fibroblast subpopulations and discern their spatial location within the synovium. We envision that this instrument will have broad utility in both research and clinical settings, enabling low-cost and routine application of microfluidic techniques.

PMID:
29476078
PMCID:
PMC5824814
DOI:
10.1038/s41467-017-02659-x
[Indexed for MEDLINE]
Free PMC Article

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