PXD058342-1

PXD058342 is an original dataset announced via ProteomeXchange.

Title	The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow
Description	A label-free proteomics dataset from our investigation of the interplay of constitutive gene-body CpG methylation (gbM), tRNA abundance and codon composition on mRNA and protein expression, in the plant Arabidopsis thaliana. We performed genomic profiling in rosette leaves of two Arabidopsis accessions, Col-0 and Can-0, and re-assembled and re-annotated their genomes using long reads. We measured gene and protein expression levels in multiple biological replicates grown in a constant environment, also measuring ribosome-associated transcript levels and tRNA abundance. We fitted models to explain variation in gbM, tRNA, gene and protein expression in the paper.
HostingRepository	PRIDE
AnnounceDate	2025-07-31
AnnouncementXML	Submission_2025-07-31_09:36:47.059.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yong-In Kim
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-27 10:13:31	ID requested
⏵ 1	2025-07-31 09:36:47	announced

Dataset with its publication pending

submitter keyword: DIA,Arabidopsis, Leaf, diaPASEF, Can-0, Col-0

Kathryn S.
contact affiliation	Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR UK
contact email	ksl23@cam.ac.uk
lab head
Yong-In Kim
contact affiliation	University of Cambridge
contact email	yk396@cam.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD058342
     1. Label: PRIDE project
     2. Name: The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow