PXD058242-1
PXD058242 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines |
| Description | Translation is the process by which genetic information from mRNA is decoded to produce proteins. Since mRNA levels alone do not predict protein amounts accurately, understanding translational control is essential. Ribosome profiling revealed that translation initiation is the main rate-limiting step, with rates varying up to 100-fold across mRNAs, while elongation rates vary less (~20-fold). Furthermore, only a small fraction of the variation in translation rates is explained by known determinants, indicating that much remains to be understood in the prediction of protein outputs of individual mRNAs. Current machine learning models would benefit from more data on endogenous mRNAs. To address this, here we report steady-state and dynamic multi-omics data from human liver cancer cell lines, specifically i) ribosome profiling of unperturbed cells and following translation initiation block to trace elongation (run-off ribosome profiling), ii) protein synthesis rates estimated by pulsed stable isotope labeled amino acids in cell culture (pSILAC), and iii) mean ribosome load on individual mRNAs determined by mRNA sequencing of polysome fractions (polysome profiling). Predicting protein output from mRNAs is crucial for applications like protein expression engineering or mRNA vaccine designing. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-06-25 |
| AnnouncementXML | Submission_2025-06-25_04:55:47.776.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Alex Schmidt |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-11-25 07:40:59 | ID requested | |
| ⏵ 1 | 2025-06-25 04:55:48 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: SWATH, DIA, pSILAC, mRNA, polysome profiling, DatasetType:Proteomics |
Contact List
| Alexander Schmidt | |
|---|---|
| contact affiliation | Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland |
| contact email | alex.schmidt@unibas.ch |
| lab head | |
| Alex Schmidt | |
| contact affiliation | University of Basel |
| contact email | alex.schmidt@unibas.ch |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive-ftp.ucsd.edu/v07/MSV000096514/ |
to receive all new ProteomeXchange dataset release announcements!
