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Series GSE10364 Query DataSets for GSE10364
Status Public on Mar 28, 2008
Title Small RNA profile in fully grown mammalian oocytes
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary We aim to comprehensively characterize the small RNA population in oocytes
Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. In at least one case, an inverted repeat pseudogene gives rise to abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting in concert with piwi-interacting RNAs (piRNAs). Loss of Dicer increases expression of endo-siRNA targets, demonstrating the regulatory activity of these small RNAs. Our findings provide a function for pseudogenes in regulating gene expression via the RNAi pathway and may, in part, explain the evolutionary pressure to conserve Argonaute-mediated catalysis in mammals.
Keywords: small RNAs profile
Overall design Total RNA was isolated and size-fractionated by PAGE either into 19-24nt and 24-30nt, or 19-30nt. These were independently processed and sequenced on Illumina 1G platform.
Contributor(s) Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachindanandam R, Schultz RM, Hannon GJ
Citation(s) 18404147
Submission date Feb 01, 2008
Last update date May 15, 2019
Contact name ravi Sachidanandam
Phone 516 367 8864
Fax 516 367 8389
Organization name Cold Spring Harbor Laboratory
Department N/A
Lab sachidanandam
Street address 1 bungtown road
City Cold spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (3)
GSM261957 oocytesmallRNA-19to24
GSM261958 oocytesmallRNA-24to30
GSM261959 oocytesmallRNA-19to30
SRA SRP000733
BioProject PRJNA105627

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
GSE10364_RAW.tar 109.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data included within Sample table
Raw data are available in SRA

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