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| Status |
Public on Sep 23, 2013 |
| Title |
Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos |
| Organism |
Xenopus tropicalis |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. We go on to identify a new class of small intronic non-coding RNAs, that we name sincRNAs. On a genome-wide scale we find that genes containing sincRNA clusters are transcriptionally repressed. Our data suggest a novel mechanism of sincRNA-mediated gene silencing in vertebrates.
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| |
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| Overall design |
Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.
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| |
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| Contributor(s) |
Harding JL, Horswell S, Armisen J, Zimmerman LB, Miska EA, Hill CS |
| Citation(s) |
24065776 |
| |
| Submission date |
Jun 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Caroline Hill |
| E-mail(s) |
[email protected]
|
| Phone |
+44 20 7269 2941
|
| Organization name |
Cancer Research UK London Research Institute
|
| Lab |
Developmental Signalling
|
| Street address |
44 Lincoln's Inn Fields
|
| City |
London |
| ZIP/Postal code |
WC2A 3LY |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL13741 |
Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA168208 |
| SRA |
SRP013627 |
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