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| Status |
Public on Mar 31, 2016 |
| Title |
Identification of small non-coding RNAs in zebrafish |
| Organism |
Danio rerio |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification; however, cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from small non-coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted.
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| Overall design |
Small RNA libraries were prepared from different zebrafish developmental stages, namely, 24 hours post-fertilization (hpf), 72 hpf, 96 hpf, 5 days post-fertilization (dpf), 45 dpf, young adult and from adult brain, eyes, gills, heart, skin and fins.
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| Contributor(s) |
Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA |
| Citation(s) |
26694924 |
| Submission date |
Mar 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ana Soares |
| E-mail(s) |
ana.r.soares@ua.pt
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| Organization name |
University of Aveiro
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| Street address |
Campus de Santiago
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| City |
Aveiro |
| ZIP/Postal code |
3810 |
| Country |
Portugal |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA277780 |
| SRA |
SRP056014 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE66718_RAW.tar |
30.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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