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Series GSE50452 Query DataSets for GSE50452
Status Public on Aug 30, 2013
Title High-throughput identification of miRNA targets using CLASH (crosslinking, ligation and sequencing of hybrids)
Organisms Saccharomyces cerevisiae; Homo sapiens
Experiment type Other
Summary Purpose: Identification of miRNA-mRNA interactions in human cells.
Method: We used the CLASH technique with PTH-tagged AGO1 protein as a bait.
Results: In 6 experiments we identified more than 18,000 miRNA-mRNA interactions in human HEK293 cells, corresponding to targets of 399 miRNAs.
Conclusions: 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.
Overall design 6 samples (E1-E6) were prepared with comparable but not identical protocols, described in more detail in Helwak et al. Cell 2013. Samples E7-E10 were used for the determination of the background of the method resulting from RNA-RNA interactions formed after cell lysis.
Contributor(s) Helwak A, Kudla G, Tollervey D
Citation(s) 23622248
Submission date Aug 29, 2013
Last update date May 15, 2019
Contact name Grzegorz Kudla
Phone +44 (0) 131 332 2471
Organization name University of Edinburgh
Department MRC HGU
Street address Crewe Road
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
Platforms (3)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL17658 Illumina MiSeq (Homo sapiens; Saccharomyces cerevisiae)
Samples (10)
GSM1219487 E1_A12
GSM1219488 E2_0727 and E2_0727HS
GSM1219489 E3_L1 and E3_L1HS
BioProject PRJNA217521
SRA SRP029351

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
GSE50452_RAW.tar 1.3 Mb (http)(custom) TAR (of TXT)
GSE50452_hyb_column_header.txt.gz 261 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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