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Series GSE38605 Query DataSets for GSE38605
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.
 
Overall design Examination of small RNAs and mRNA at 3 stages of Xenopus embryonic development.
 
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) caroline.hill@cancer.org.uk
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
 
Platforms (1)
GPL13741 Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis)
Samples (8)
GSM945997 stage 8 small RNA-seq
GSM945998 stage 10 small RNA-seq
GSM945999 stage 18 small RNA-seq
Relations
BioProject PRJNA168208
SRA SRP013627

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38605_RAW.tar 974.6 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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