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Series GSE57313 Query DataSets for GSE57313
Status Public on May 19, 2014
Title MicroRNAs Shape Circadian Hepatic Gene Expression on a Transcriptome-Wide Scale
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Introduction: A considerable proportion of mammalian gene expression undergoes circadian oscillations. Post-transcriptional mechanisms likely make important contributions to mRNA abundance rhythms.
Aim: We have investigated how microRNAs contribute to core clock and clock-controlled gene expression using mice in which microRNA biogenesis can be inactivated in the liver.
Results: While the hepatic core clock was surprisingly resilient to microRNA loss, whole transcriptome sequencing uncovered widespread effects on clock ouput gene expression. Cyclic transcription paired with microRNA-mediated regulation was thus identified as a widespread phenomenon that affected up to 30% of the rhythmic transcriptome and served to post-transcriptionally adjust the phases and amplitudes of rhythmic mRNA accumulation. However, only a few mRNA rhythms were actually generated by microRNAs. Finally, we pinpoint several microRNAs predicted to act as modulators of rhythmic transcripts, and identify rhythmic pathways particularly prone to microRNA regulation.
Conclusion: Our study provides a comprehensive analysis of miRNA activity in shaping hepatic circadian gene expression and can serve as a valuable resource for further investigations into the regulatory roles that miRNAs play in liver gene expression and physiology.
 
Overall design RNA-Seq of rRNA-depleted total RNAs from two independent full time series around-the-clock of Dicer knockout and control mouse livers
 
Contributor(s) Du NH, Arpat AB, De Matos M, Gatfield D
Citation(s) 24867642
Submission date May 05, 2014
Last update date May 15, 2019
Contact name David Gatfield
E-mail(s) david.gatfield@unil.ch
Phone +41 21 692 39 94
Organization name University of Lausanne
Department CIG
Street address UNIL CIG
City Lasuanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (24)
GSM1379389 Dcr1
GSM1379390 Dcr2
GSM1379391 Dcr3
Relations
BioProject PRJNA246230
SRA SRP041679

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57313_Mmusculus_v1.1_flatten.gtf.gz 3.1 Mb (ftp)(http) GTF
GSE57313_RAW.tar 7.5 Mb (http)(custom) TAR (of RPKM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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