Single cell RNA sequencing of stem cell-derived retinal ganglion cells

Maciej Daniszewski; Anne Senabouth; Quan H Nguyen; Duncan E Crombie; Samuel W Lukowski; Tejal Kulkarni; Valentin M Sluch; Jafar S Jabbari; Xitiz Chamling; Donald J Zack; Alice Pébay; Joseph E Powell; Alex W Hewitt

doi:10.1038/sdata.2018.13

Single cell RNA sequencing of stem cell-derived retinal ganglion cells

Sci Data. 2018 Feb 13:5:180013. doi: 10.1038/sdata.2018.13.

Authors

Maciej Daniszewski^{1

2}, Anne Senabouth³, Quan H Nguyen³, Duncan E Crombie^{1

2}, Samuel W Lukowski³, Tejal Kulkarni^{1

2}, Valentin M Sluch⁴, Jafar S Jabbari⁵, Xitiz Chamling⁴, Donald J Zack^{4

6}, Alice Pébay^{1

2}, Joseph E Powell^{3

7}, Alex W Hewitt^{1

2

8}

Affiliations

¹ Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne 3002, Australia.
² Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne 3002, Australia.
³ Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4067, Australia.
⁴ Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁵ Australian Genome Research Facility, Melbourne 3051, Australia.
⁶ Departments of Neuroscience, Molecular Biology and Genetics, and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
⁷ Queensland Brain Institute, University of Queensland, St Lucia, Brisbane 4072, Australia.
⁸ School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart 7000, Australia.

Abstract

We used single cell sequencing technology to characterize the transcriptomes of 1,174 human embryonic stem cell-derived retinal ganglion cells (RGCs) at the single cell level. The human embryonic stem cell line BRN3B-mCherry (A81-H7), was differentiated to RGCs using a guided differentiation approach. Cells were harvested at day 36 and prepared for single cell RNA sequencing. Our data indicates the presence of three distinct subpopulations of cells, with various degrees of maturity. One cluster of 288 cells showed increased expression of genes involved in axon guidance together with semaphorin interactions, cell-extracellular matrix interactions and ECM proteoglycans, suggestive of a more mature RGC phenotype.

Publication types

Dataset
Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Cell Differentiation
Cell Line
Embryonic Stem Cells* / cytology
Embryonic Stem Cells* / physiology
Humans
RNA / genetics*
Retinal Ganglion Cells* / cytology
Retinal Ganglion Cells* / physiology
Sequence Analysis, RNA
Single-Cell Analysis

Substances

RNA

Associated data

figshare/10.6084/m9.figshare.5715148

Grants and funding

T32 GM007445/GM/NIGMS NIH HHS/United States