<<< Full experiment listing


PXD014484 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIdentification of functional miRNA gene interactions in mESC by computational data integration approaches.
DescriptionmiRNAs are short regulatory single stranded RNA sequences that upon complementary binding to mRNAs lead to the inhibition or degradation of their targets. This regulatory mechanisms has been shown to play crucial roles throughout the whole life cycle of animals and plants as well as in disease. While a plethora of methods exist to predict targets of miRNA, which suggest that up to 80% of the genome is miRNA regulated, it has recently been reported that many of these predictions are false positives, cell type specific or represent non-functional binding. In order to identify the subset of real functional miRNAs and their targets, we established miRNA pathway mutants in mouse embryonic stem cells (mESC), allowing the dissection of canonical and non-canonical functions of pathway members. Additional data integration of downstream regulatory layers (CLIP-seq, ribosome profiling and MS) enabled us to follow and track down real functional miRNA-gene interactions, which reduced the miRNA genome regulation to approximately 1%.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTatjana Sajic
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-07-04 04:17:38ID requested
12022-08-31 11:12:23announced
Publication List
Schaefer M, Nabih A, Spies D, Hermes V, Bodak M, Wischnewski H, Stalder P, Ngondo RP, Liechti LA, Sajic T, Aebersold R, Gatfield D, Ciaudo C, Global and precise identification of functional miRNA targets in mESCs by integrative analysis. EMBO Rep, 23(9):e54762(2022) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: mouse, stem cells, miRNA, transcriptomics, ribosome profiling, proteomics, mass spectrometry, data integration
Contact List
Prof. Dr. Rudolf Aebersold
contact affiliationETH Zurich Inst. f. Molekulare Systembiologie
contact emailaebersold@imsb.biol.ethz.ch
lab head
Tatjana Sajic
contact affiliationIMSB, ETH Zurich
contact emailsajic@imsb.biol.ethz.ch
dataset submitter
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/08/PXD014484
PRIDE project URI
Repository Record List
[ + ]