PXD014484-1

PXD014484 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-04 04:17:38	ID requested
⏵ 1	2022-08-31 11:12:23	announced
2	2024-10-22 05:39:31	announced	2024-10-22: Updated project metadata.

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]

curator keyword: Biological

submitter keyword: mouse, stem cells, miRNA, transcriptomics, ribosome profiling, proteomics, mass spectrometry, data integration

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

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

• PRIDE
  1. PXD014484
     1. Label: PRIDE project
     2. Name: Identification of functional miRNA gene interactions in mESC by computational data integration approaches.