PXD052353-1

PXD052353 is an original dataset announced via ProteomeXchange.

Title	Epigenomic, transcriptomic and proteomic characterizations of reference samples
Description	A variety of newly developed next-generation sequencing technologies are making their way rapidly into the research and clinical applications, for which accuracy and cross-lab reproducibility are critical, and reference standards are much needed. However, there is still a lack of well-characterized reference materials which include epigenomic and proteomic data. Our previous multicenter studies under the SEQC-2 umbrella using a breast cancer cell line with paired B-cell line have produced large amount different genomic data including whole genome sequencing (Illumina, PacBio, Nanopore), HiC, and scRNA-seq with detailed analyses on somatic mutations, single-nucleotide variations (SNVs), and structure variations (SVs). Here we further performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses and provided a comprehensive catalog of epigenomic landscape, which overlapped with the transcriptomes and proteomes for the two cell lines. We identified >7,700 peptide isoforms, where the majority (95%) of the genes had a single peptide isoform and found that the protein expression levels of the transcripts overlapping CGIs were much higher than the protein expression levels of the non-CGI transcripts in both cell lines. We observed that open chromatin regions had low methylation while closed chromatin regions had high methylation, which were largely regulated by CG density, where CG-rich regions had more accessible chromatin, low methylation, and higher gene and protein expressions. The CG-poor regions had higher repressive epigenetic regulations (less open chromatin and higher DNA methylation), resulting in a cell line specific methylation and gene expression patterns. Our studies provide well-defined reference materials consisting of two cell lines with genomic, epigenomic, transcriptomic, scRNA-seq and proteomic characterizations which can serve as standards for validating and benchmarking not only on various omics assays, but also on bioinformatics methods. It will be a valuable resource for both research and clinical communities.
HostingRepository	PRIDE
AnnounceDate	2025-10-06
AnnouncementXML	Submission_2025-10-06_12:20:51.531.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ling Xie
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-17 08:05:00	ID requested
⏵ 1	2025-10-06 12:20:52	announced

Dataset with its publication pending

submitter keyword: omics assays, Q Exactuve HF-X,human

Charles Wang
contact affiliation	Center for Genomics Department of Basic Sciences Loma Linda University School of Medicine
contact email	chwang@llu.edu
lab head
Ling Xie
contact affiliation	UNC at Chapel Hill
contact email	xiel@email.unc.edu
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/2025/10/PXD052353

PRIDE project URI

• PRIDE
  1. PXD052353
     1. Label: PRIDE project
     2. Name: Epigenomic, transcriptomic and proteomic characterizations of reference samples