E-GEOD-38605 - Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

Released on 23 September 2013, last updated on 3 October 2013
Xenopus (Silurana) tropicalis
Samples (8)
Protocols (5)
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. Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.
Experiment types
RNA-seq of coding RNA, RNA-seq of non coding RNA 
Caroline Hill <caroline.hill@cancer.org.uk>, Caroline S Hill, Eric A Miska, Javier Armisen, Joanne L Harding, Lyle B Zimmerman, Stuart Horswell
Exp. designProtocolsVariablesProcessedSeq. reads