Uncovering the temporal gene expression dynamics of phytoplankton with single cell RNA sequencing.

  • Funding College of Science, Nanyang technological University – Singapore
  • Role: Co-Principal Investigator
  • Period: 2021 – 2022

This project aims to introduce Drop-Seq to study the diurnal gene expression in marine phytoplankton. Drop-Seq, a “in house” microfluidic device, analyzes mRNA transcripts fromdroplets of individual cells in a highly parallel fashion. This single-cell sequencing method uses a microfluidic device to compartmentalize droplets containing a single cell, lysis buffer, and a microbead covered with barcoded primers. Drop-Seq allows us to capture the gene expression of individual phytoplanktonic cells by seizing the different gene expression states of each individual under the diurnal cycle. Studying the cell cycle can tell us a great deal about how a cell works and the mechanisms controlling its division, but this information is limited to very few phytoplankton species as typical experiments require the collection of many RNA-seq samples, which can be economically prohibitive. To this end, we have built a Drop-Seq microfluidic device, and we will use it to study the cell cycle of model phytoplankton species from 2 distinct green lineage classes representing phytoplankton from coastal, oceanic, polar and tropical waters: Mamiellophyceae (one of the main phytoplankton group found in Singapore waters5) and Chloropicophyceae (the oceanic counterpart). Importantly, while typical cell cycle experiments require 18 RNA-seq samples to analyze gene expression of one species, our modified protocol has the potential to provide a detailed analysis of the diurnal gene expression for multiple species with just one RNA-seq analysis.

Principal Investigator

Adriana Lopes dos Santos
Adriana Lopes dos Santos
Assistant Professor