Single-cell transcriptomics of small microbial eukaryotes: limitations and potential. Academic Article

abstract

• Single-cell transcriptomics is an emerging research tool that has huge untapped potential in the study of microbial eukaryotes. Its application has been tested in microbial eukaryotes 50m or larger, and it generated transcriptomes similar to those obtained from culture-based RNA-seq. However, microbial eukaryotes have a wide range of sizes and can be as small as 1m. Single-cell RNA-seq was tested in two smaller protists (8 and 15m). Transcript recovery rate was much lower and randomness in observed gene expression levels was much higher in single-cell transcriptomes than those derived from bulk cultures of cells. We found that the reason of such observation is that the smaller organisms had much lower mRNA copy numbers. We discuss the application of single-cell RNA-seq in studying smaller microbial eukaryotes in the context of these limitations.

authors

• Hu, Sarah

published proceedings

• ISME J

altmetric score

• 13.7

author list (cited authors)

• Liu, Z., Hu, S. K., Campbell, V., Tatters, A. O., Heidelberg, K. B., & Caron, D. A.

citation count

• 41

complete list of authors

• Liu, Zhenfeng||Hu, Sarah K||Campbell, Victoria||Tatters, Avery O||Heidelberg, Karla B||Caron, David A

publication date

• May 2017

publisher

• Oxford University Press (OUP)  Publisher

published in

• The ISME Journal  Journal

keywords

• Dinoflagellida
• Gene Expression Profiling
• Haptophyta
• RNA, Messenger
• Sequence Analysis, RNA
• Single-Cell Analysis
• Transcriptome

PubMed Central ID

• 28060364

Digital Object Identifier (DOI)

• 10.1038/ismej.2016.190

start page

• 1282

end page

• 1285

volume

• 11

issue

• 5

URL

• http://dx.doi.org/10.1038/ismej.2016.190