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GEO Series: GSE38605

Title: Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

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.


Contributors: Caroline Hill, Joanne Harding, Stuart Horswell, Javier Armisen, Lyle Zimmerman, Eric Miska, Caroline Hill

Experiment Type: Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.

Article: XB-ART-47876, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF10 GSM946003  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF10 small RNA GSM945998  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF18 GSM946004  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 18  
WE - NF18 small RNA GSM945999  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 18  
WE - NF8 GSM946002  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 small RNA GSM945997  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
animal pole - NF10 GSM946000  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
animal pole NF stage 10  
vegetal pole - NF10 GSM946001  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal pole NF stage 10  
Select All 
Xtr   
Xla 

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