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| Status |
Public on Sep 06, 2009 |
| Title |
Illumina sequencing of small RNAs from C. elegans embryos |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect large amounts of cleanly staged C. elegans embryos by Fluorescent Activated Cell Sorting (termed eFACS). eFACS can in principle be applied to all embryonic developmental stages up to hatching. As a proof of principle we show that a single eFACS run routinely yields tens of thousands of almost perfectly staged one-cell embryos. Since in animals the earliest embryonic events are driven by post-transcriptional regulation, we combined eFACS with next-generation sequencing technology to systematically profile the embryonic expression of small, non-coding RNAs. We discovered a wealth of complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including miRNAs, during embryogenesis. Our data indicate that half of all known miRNAs are already expressed in the one-cell stage embryo and we also shed light on the expression and genomic organization of the previously under-appreciated 26G-RNAs. Together, our eFACS data suggest that the complexity of small RNA expression dynamics in animals is comparable to the expression dynamics of protein encoding genes.
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| Overall design |
Various C. elegans embryo samples were generated: mixed embryos by traditional bleaching (Brenner, 1974), early embryos by eFACS (Stoeckius et al., in press). RNA was extracted and length fractionated. Small RNA was subjected to a 5'-dependent ligation protocol to add sequencing adapters. The small RNA samples were sequenced using the Illumina GA I & II.
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| Contributor(s) |
Stoeckius M, Maaskola J, Colombo T, Rahn H, Friedländer MR, Li N, Chen W, Piano F, Rajewsky N |
| Citation(s) |
19734907 |
| |
| Submission date |
Jul 16, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonas Maaskola |
| Organization name |
Max-Delbrueck Centrum Berlin-Buch
|
| Department |
Systems Biology of Gene Regulatory Elements
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| Lab |
Rajewsky
|
| Street address |
Robert-Roessle Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platforms (1) |
| GPL9269 |
Illumina Genome Analyzer II (Caenorhabditis elegans) |
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| Samples (6)
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| GSM427297 |
Illumina sequencing of small RNAs from two-to-four cell C. elegans embryos |
| GSM427301 |
Illumina sequencing of small RNAs from one cell stage C. elegans embryos |
| GSM427332 |
Illumina sequencing of small RNAs from post-gastrulation C. elegans embryos |
| GSM427344 |
Illumina sequencing of small RNAs from older, fixed C. elegans embryos |
| GSM427345 |
Illumina sequencing of small RNAs from living one cell C. elegans embryos |
| GSM427346 |
Illumina sequencing of small RNAs from mixed C. elegans embryos |
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| Relations |
| SRA |
SRP001363 |
| BioProject |
PRJNA119753 |
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