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Series GSE97056 Query DataSets for GSE97056
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 (Human CLIP-Seq)
Organism Homo sapiens
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
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)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (28)
GSM2550604 Patient 1 Normal 1
GSM2550605 Patient 1 Normal 2
GSM2550606 Patient 2 Normal 1
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
BioProject PRJNA380701
SRA SRP102610

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Supplementary file Size Download File type/resource
GSE97056_HumanLiver_AgoCLIP_Matrix.txt.gz 4.1 Mb (ftp)(http) TXT
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