Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression

Marlon Stoeckius, Jonas Maaskola, Teresa Colombo, Hans Peter Rahn, Marc R. Friedländer, Na Li, Wei Chen, Fabio Piano, Nikolaus Rajewsky

Research output: Contribution to journalArticle

Abstract

Caenorhabditis elegans is one of the most prominent model systems for embryogenesis, but collecting many precisely staged embryos has been impractical. Thus, early C. elegans embryogenesis has not been amenable to most high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect staged C. elegans embryos by fluorescence-activated cell sorting (eFACS). In a proof-of-principle experiment, we found that a single eFACS run routinely yielded tens of thousands of almost perfectly staged 1-cell stage embryos. As the earliest embryonic events are driven by posttranscriptional regulation, we combined eFACS with second-generation sequencing to profile the embryonic expression of small, noncoding RNAs. We discovered complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including microRNAs and 26G-RNAs, during embryogenesis.

Original languageEnglish (US)
Pages (from-to)745-751
Number of pages7
JournalNature Methods
Volume6
Issue number10
DOIs
StatePublished - 2009

Fingerprint

Sorting
Embryonic Structures
Fluorescence
RNA
Caenorhabditis elegans
Embryonic Development
Flow Cytometry
Small Untranslated RNA
Biochemistry
MicroRNAs
Assays
Cells
Throughput
Genomics
Experiments

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Stoeckius, M., Maaskola, J., Colombo, T., Rahn, H. P., Friedländer, M. R., Li, N., ... Rajewsky, N. (2009). Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nature Methods, 6(10), 745-751. https://doi.org/10.1038/nmeth.1370

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. / Stoeckius, Marlon; Maaskola, Jonas; Colombo, Teresa; Rahn, Hans Peter; Friedländer, Marc R.; Li, Na; Chen, Wei; Piano, Fabio; Rajewsky, Nikolaus.

In: Nature Methods, Vol. 6, No. 10, 2009, p. 745-751.

Research output: Contribution to journalArticle

Stoeckius, M, Maaskola, J, Colombo, T, Rahn, HP, Friedländer, MR, Li, N, Chen, W, Piano, F & Rajewsky, N 2009, 'Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression', Nature Methods, vol. 6, no. 10, pp. 745-751. https://doi.org/10.1038/nmeth.1370
Stoeckius M, Maaskola J, Colombo T, Rahn HP, Friedländer MR, Li N et al. Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nature Methods. 2009;6(10):745-751. https://doi.org/10.1038/nmeth.1370
Stoeckius, Marlon ; Maaskola, Jonas ; Colombo, Teresa ; Rahn, Hans Peter ; Friedländer, Marc R. ; Li, Na ; Chen, Wei ; Piano, Fabio ; Rajewsky, Nikolaus. / Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. In: Nature Methods. 2009 ; Vol. 6, No. 10. pp. 745-751.
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