PXD037866

PXD037866 is an original dataset announced via ProteomeXchange.

Title	PRM of eGFP and mCherry in human cells
Description	We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. In particular, we detect two clusters of tissues with an opposite pattern of codon preferences. We then use the identified patterns for the development of CUSTOM (https://custom.crg.eu), a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In a human cell model, we provide evidence that codon optimization should indeed take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:59:52.381.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xavier Hernandez Alias
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-31 09:27:50	ID requested
1	2023-02-24 06:47:42	announced
2	2023-02-27 06:47:45	announced	2023-02-27: Updated project metadata.
3	2023-11-14 07:25:35	announced	2023-11-14: Updated project metadata.
⏵ 4	2023-11-14 08:59:53	announced	2023-11-14: Updated project metadata.

Hernandez-Alias X, Benisty H, Radusky LG, Serrano L, Schaefer MH, Using protein-per-mRNA differences among human tissues in codon optimization. Genome Biol, 24(1):34(2023) [pubmed]

submitter keyword: LC-MSMS, PRM, lung, kidney,human

Luis Serrano
contact affiliation	Systems Biology Unit, Design of Biological Systems, Centre for Genomic Regulation (CRG), Spain
contact email	luis.serrano@crg.eu
lab head
Xavier Hernandez Alias
contact affiliation	Centre de Regulació Genòmica
contact email	xavier.hernandez@crg.eu
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/2023/02/PXD037866

PRIDE project URI

• PRIDE
  1. PXD037866
     1. Label: PRIDE project
     2. Name: PRM of eGFP and mCherry in human cells