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Series GSE20048 Query DataSets for GSE20048
Status Public on Feb 27, 2010
Title Genome-wide Identification of Targets & Function of Individual MicroRNAs in Mouse Embryonic Stem Cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays, and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-Sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs, and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes, and upregulating pluripotency-associated genes such as Lin28.
 
Overall design Cells were co-transfected (Amaxa nucleofection) with 300pmol of microRNA and 1 microgram of pEGFP-1, which served as a control for transfection efficiency. GFP-positive cells were sorted 24 hours after transfection. We profiled the transcriptome of Dicer1-null mouse ES cells transfected with miR-294 or a control microRNA (cel-239b), using the Illumina WG-6 v2.0 platform.
 
Contributor(s) Hanina SA, Mifsud W, Surani MA
Citation(s) 20975942
Submission date Jan 26, 2010
Last update date Jan 16, 2019
Contact name Sophie Alexandra Hanina
Organization name University of Cambridge
Department Gurdon Institute
Street address Tennis Court Road
City Cambridge
State/province Cambridgeshire
ZIP/Postal code CB2 1QN
Country United Kingdom
 
Platforms (1)
GPL6887 Illumina MouseWG-6 v2.0 expression beadchip
Samples (6)
GSM501210 ES cells + control microRNA replicate 1
GSM501211 ES cells + control microRNA replicate 2
GSM501212 ES cells + control microRNA replicate 3
Relations
BioProject PRJNA124311

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
GSE20048_RAW.tar 15.8 Mb (http)(custom) TAR
GSE20048_non-normalized.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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