PXD064017-1

PXD064017 is an original dataset announced via ProteomeXchange.

Title	Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Phosphoproteomics]
Description	Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.
HostingRepository	PRIDE
AnnounceDate	2025-06-18
AnnouncementXML	Submission_2025-06-18_00:57:50.941.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ying-Chung Jimmy Lin
SpeciesList	scientific name: Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa); NCBI TaxID: 3694;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-16 08:46:00	ID requested
⏵ 1	2025-06-18 00:57:51	announced

Dataset with its publication pending

submitter keyword: Mechanical Stress,Xylem Development, Tension Wood, Cell Fate Determination, LC-MS/MS, Phosphoproteome, Gravity Sensing

Ying-Chung Jimmy
contact affiliation	Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
contact email	ycjimmylin@ntu.edu.tw
lab head
Ying-Chung Jimmy Lin
contact affiliation	Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
contact email	ycjimmylin@ntu.edu.tw
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/2025/06/PXD064017

PRIDE project URI

• PRIDE
  1. PXD064017
     1. Label: PRIDE project
     2. Name: Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Phosphoproteomics]