Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.
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) tec...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0296672&type=printable |
| _version_ | 1797349338860486656 |
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| author | Vesna Grujčić Sami Saarenpää John Sundh Bengt Sennblad Benjamin Norgren Meike Latz Stefania Giacomello Rachel A Foster Anders F Andersson |
| author_facet | Vesna Grujčić Sami Saarenpää John Sundh Bengt Sennblad Benjamin Norgren Meike Latz Stefania Giacomello Rachel A Foster Anders F Andersson |
| author_sort | Vesna Grujčić |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T12:28:53Z |
| format | Article |
| id | doaj.art-060865f271f340c1ba9c4f9913e88455 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-08T12:28:53Z |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-060865f271f340c1ba9c4f9913e884552024-01-22T05:31:26ZengPublic Library of Science (PLoS)PLoS ONE1932-62032024-01-01191e029667210.1371/journal.pone.0296672Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.Vesna GrujčićSami SaarenpääJohn SundhBengt SennbladBenjamin NorgrenMeike LatzStefania GiacomelloRachel A FosterAnders F AnderssonSingle-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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0296672&type=printable |
| spellingShingle | Vesna Grujčić Sami Saarenpää John Sundh Bengt Sennblad Benjamin Norgren Meike Latz Stefania Giacomello Rachel A Foster Anders F Andersson Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. PLoS ONE |
| title | Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. |
| title_full | Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. |
| title_fullStr | Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. |
| title_full_unstemmed | Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. |
| title_short | Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton. |
| title_sort | towards high throughput parallel imaging and single cell transcriptomics of microbial eukaryotic plankton |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0296672&type=printable |
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