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E-GEOD-46039 - hsa-miR-92a knock down in Flp-in T-REx 293-PTH-AGO1 cells

Status
Released on 26 April 2013, last updated on 7 May 2013
Organism
Homo sapiens
Samples (10)
Array (1)
Protocols (7)
Description
transcriptome profiling of miR-92a inhibitor treated and control cells with the aim of measuring miR-92a influence on its mRNA targets Abstract: MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human Ago1. Here we report datasets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, non-seed basepairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA basepairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding. In total 10 samples were analyzed, 5 repeats for each experimental condition.
Experiment type
transcription profiling by array 
Contacts
Grzegorz Kudla <gkudla@gmail.com>, Aleksandra Helwak, David Tollervey
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-46039.idf.txt
Sample and data relationshipE-GEOD-46039.sdrf.txt
Raw data (2)E-GEOD-46039.raw.1.zip, E-GEOD-46039.raw.2.zip
Processed data (1)E-GEOD-46039.processed.1.zip
Array designA-AFFY-143.adf.txt
Links