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Series GSE97060 Query DataSets for GSE97060
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 RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
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)
GSM2550655 KO Female 1 RNAseq
GSM2550656 KO Male 2 RNAseq
GSM2550657 KO Male 3 RNAseq
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 PRJNA380616
SRA SRP102517

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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
GSE97060_122KOMouse_SleuthOutput.txt.gz 1.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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