PXD014484 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Identification of functional miRNA gene interactions in mESC by computational data integration approaches. |
Description | miRNAs 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%. |
HostingRepository | PRIDE |
AnnounceDate | 2022-08-31 |
AnnouncementXML | Submission_2022-08-31_11:12:23.009.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Tatjana Sajic |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-07-04 04:17:38 | ID requested | |
⏵ 1 | 2022-08-31 11:12:23 | announced | |
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 affiliation | ETH Zurich Inst. f. Molekulare Systembiologie |
contact email | aebersold@imsb.biol.ethz.ch |
lab head | |
Tatjana Sajic |
contact affiliation | IMSB, ETH Zurich |
contact email | sajic@imsb.biol.ethz.ch |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD014484
- Label: PRIDE project
- Name: Identification of functional miRNA gene interactions in mESC by computational data integration approaches.