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GEO Series: GSE30067

Title: Deep sequencing of small RNAs in the Xenopus tropicalis gastrula

Summary

Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous siRNAs and piRNAs. In order to determine if small RNAs mapped to expressed Tc1-like elements are present during early Xenopus tropicalis development, we used Illumina (Solexa) to sequence small RNAs from gastrula-stage embryos. We obtained about 17 million reads that mapped perfectly to the genome. Small RNAs mapped to selected transposable elements were characterized and the expression of selected small RNAs was experimentally verified during development. This is the first deep sequencing experiment for small RNAs in the Xenopus tropicalis gastrula.


Contributors: Juan Larrain, Fernando Faunes, Natalia Sanchez, Mauricio Moreno, Gonzalo Olivares, Dasfne Lee-Liu, Leonardo Almonacid, Alex Slater, Tomas Norambuena, Ryan Taft, John Mattick, Francisco Melo

Experiment Type: Analysis of small RNAs expressed in the Xenopus tropicalis gastrula.

Article: XB-ART-43632, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
dorsal WE - NF10 GSM744253  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
dorsal NF stage 10  
embryo NF stage 10  
ventral WE - NF10 GSM744254  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
ventral NF stage 10  
Select All 
Xtr   
Xla 

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