title: Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells.
abstract: This study provides an assessment of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. The system combines microfluidic technology and nanoliter-scale reactions. We sequenced 622 cells, allowing identification of 341 islet cells with high-quality gene expression profiles. The cells clustered into populations of α-cells (5%), β-cells (92%), δ-cells (1%), and pancreatic polypeptide cells (2%). We identified cell-type-specific transcription factors and pathways primarily involved in nutrient sensing and oxidation and cell signaling. Unexpectedly, 281 cells had to be removed from the analysis due to low viability, low sequencing quality, or contamination resulting in the detection of more than one islet hormone. Collectively, we provide a resource for identification of high-quality gene expression datasets to help expand insights into genes and pathways characterizing islet cell types. We reveal limitations in the C1 Fluidigm cell capture process resulting in contaminated cells with altered gene expression patterns. This calls for caution when interpreting single-cell transcriptomics data using the C1 Fluidigm system.
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Yurong
authors.initials: Y
authors.lastname: Xin
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Jinrang
authors.initials: J
authors.lastname: Kim
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Min
authors.initials: M
authors.lastname: Ni
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wei
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Haruka
authors.initials: H
authors.lastname: Okamoto
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Joseph
authors.initials: J
authors.lastname: Lee
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Christina
authors.initials: C
authors.lastname: Adler
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Katie
authors.initials: K
authors.lastname: Cavino
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Murphy
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591 george@regeneron.com Jesper.Gromada@regeneron.com.
authors.forename: George D
authors.initials: GD
authors.lastname: Yancopoulos
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591.
authors.forename: Hsin Chieh
authors.initials: HC
authors.lastname: Lin
authors.affiliation: Regeneron Pharmaceuticals, Tarrytown, NY 10591 george@regeneron.com Jesper.Gromada@regeneron.com.
authors.forename: Jesper
authors.initials: J
authors.lastname: Gromada
mesh_terms: D000818:Animals; D007515:Islets of Langerhans / Q000166:cytology / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D017423:Sequence Analysis, RNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors
keywords: Fluidigm C1; glucagon; insulin; pancreatic islet cells; single-cell RNA sequencing