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Series GSE97058 Query DataSets for GSE97058
Status Public on Mar 28, 2017
Title Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer (Mouse CLIP-Seq)
Organism Mus musculus
Experiment type Other
Summary MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the miR-122 target network remains incomplete. To this end, we performed Argonaute crosslinking immunoprecipitation (Ago-CLIP) sequencing in miR-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (HCC) and benign liver tissue to identify miRNA target sites transcriptome-wide in two species. We observed a majority of miR-122 binding on 3’-UTRs and coding exons followed by extensive binding to other genic and non-genic sites. Motif analysis of miR-122 dependent binding revealed a novel G-bulged motif in addition to canonical motifs. A large number of miR-122 targets were found to be species-specific. Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma.
 
Overall design AGO CLIP-seq libraries were generated from four miR-122 KO mice and five floxed littermate controls, all at six weeks of age.
 
Contributor(s) Luna JM, Barajas JM, Teng K, Sun H, Moore MJ, Rice CM, Darnell RB, Ghoshal K
Citation(s) 28735896
Submission date Mar 27, 2017
Last update date May 15, 2019
Contact name Joseph M Luna
E-mail(s) jluna@rockefeller.edu
Organization name The Rockefeller University
Lab Darnell
Street address 1230 York Ave #64
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (9)
GSM2550642 WT Female 1 CLIP
GSM2550643 WT Female 2 CLIP
GSM2550644 WT Female 3 CLIP
This SubSeries is part of SuperSeries:
GSE97061 Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer
Relations
BioProject PRJNA380618
SRA SRP102515

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
GSE97058_122KOMouse_CLIP_Matrix.txt.gz 5.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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