Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.

Grujčić V, Saarenpää S, Sundh J, Sennblad B, Norgren B, Latz M, Giacomello S, Foster RA, Andersson AF

PLoS ONE 19 (1) e0296672 [2024-01-19; online 2024-01-19]

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.

Bioinformatics Long-term Support WABI [Collaborative]

Bioinformatics Support, Infrastructure and Training [Collaborative]

NGI Short read [Service]

NGI Stockholm (Genomics Production) [Service]

National Genomics Infrastructure [Service]

PubMed 38241213

DOI 10.1371/journal.pone.0296672

Crossref 10.1371/journal.pone.0296672

pmc: PMC10798536
pii: PONE-D-23-10489

Publications 9.5.0