Open AccessA Novel Approach to Single Cell RNA‐Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell‐Derived Retinal Cell Types
Author(s) -
Phillips M. Joseph,
Jiang Peng,
Howden Sara,
Barney Patrick,
Min Jee,
York Nathaniel W.,
Chu LiFang,
Capowski Elizabeth E.,
Cash Abigail,
Jain Shivani,
Barlow Katherine,
Tabassum Tasnia,
Stewart Ron,
Pattnaik Bikash R.,
Thomson James A.,
Gamm David M.
Publication year - 2018
Publication title -
stem cells
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.159
H-Index - 229
eISSN - 1549-4918
pISSN - 1066-5099
DOI - 10.1002/stem.2755
Subject(s) - biology , induced pluripotent stem cell , computational biology , cell type , in silico , gene , stem cell , cell , transcriptome , gene expression , reporter gene , gene expression profiling , genetics , cell culture , microbiology and biotechnology , embryonic stem cell
Cell type‐specific investigations commonly use gene reporters or single‐cell analytical techniques. However, reporter line development is arduous and generally limited to a single gene of interest, while single‐cell RNA (scRNA)‐sequencing (seq) frequently yields equivocal results that preclude definitive cell identification. To examine gene expression profiles of multiple retinal cell types derived from human pluripotent stem cells (hPSCs), we performed scRNA‐seq on optic vesicle (OV)‐like structures cultured under cGMP‐compatible conditions. However, efforts to apply traditional scRNA‐seq analytical methods based on unbiased algorithms were unrevealing. Therefore, we developed a simple, versatile, and universally applicable approach that generates gene expression data akin to those obtained from reporter lines. This method ranks single cells by expression level of a bait gene and searches the transcriptome for genes whose cell‐to‐cell rank order expression most closely matches that of the bait. Moreover, multiple bait genes can be combined to refine datasets. Using this approach, we provide further evidence for the authenticity of hPSC‐derived retinal cell types. S tem C ells 2018;36:313–324