IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-05134-3.html
   My bibliography  Save this article

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

Author

Listed:
  • Bruce A. Rheaume

    (University of Connecticut School of Medicine)

  • Amyeo Jereen

    (University of Connecticut School of Medicine)

  • Mohan Bolisetty

    (The Jackson Laboratory for Genomic Medicine)

  • Muhammad S. Sajid

    (University of Connecticut School of Medicine)

  • Yue Yang

    (University of Connecticut School of Medicine)

  • Kathleen Renna

    (University of Connecticut School of Medicine)

  • Lili Sun

    (The Jackson Laboratory for Genomic Medicine)

  • Paul Robson

    (The Jackson Laboratory for Genomic Medicine
    Institute for Systems Genomics and Department of Genetics & Genome Sciences, University of Connecticut School of Medicine)

  • Ephraim F. Trakhtenberg

    (University of Connecticut School of Medicine)

Abstract

Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified to date. Here, we analyze 6225 RGCs (average of 5000 genes per cell) from right and left eyes by single-cell RNA-seq and classify them into 40 subtypes using clustering algorithms. We identify additional subtypes and markers, as well as transcription factors predicted to cooperate in specifying RGC subtypes. Zic1, a marker of the right eye-enriched subtype, is validated by immunostaining in situ. Runx1 and Fst, the markers of other subtypes, are validated in purified RGCs by fluorescent in situ hybridization (FISH) and immunostaining. We show the extent of gene expression variability needed for subtype segregation, and we show a hierarchy in diversification from a cell-type population to subtypes. Finally, we present a website for comparing the gene expression of RGC subtypes.

Suggested Citation

  • Bruce A. Rheaume & Amyeo Jereen & Mohan Bolisetty & Muhammad S. Sajid & Yue Yang & Kathleen Renna & Lili Sun & Paul Robson & Ephraim F. Trakhtenberg, 2018. "Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes," Nature Communications, Nature, vol. 9(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05134-3
    DOI: 10.1038/s41467-018-05134-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-05134-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-05134-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yunpei Xu & Shaokai Wang & Qilong Feng & Jiazhi Xia & Yaohang Li & Hong-Dong Li & Jianxin Wang, 2024. "scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05134-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.