Evidence map›Paper›PMID 41539304›Full record

ArticleCell reports methods2026

Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.

Chirag Nepal, Wanqiu Chen, Zhong Chen, John A Wrobel, Ling Xie, Wenjing Liao, Chunlin Xiao, Adrew Farmer, Malcolm Moos, Wendell Jones and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Chirag NepalCenter for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA; Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.
Wanqiu ChenCenter for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA; Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.
Zhong ChenCenter for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA; Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.
John A WrobelDepartment of Biochemistry and Biophysics and Proteomic Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA.
Ling XieDepartment of Biochemistry and Biophysics and Proteomic Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA.
Wenjing LiaoCenter for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.
Chunlin XiaoNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20894, USA.
Adrew FarmerTakara Bio USA, Inc., San Jose, CA, USA.
Malcolm MoosCenter for Biologics Evaluation and Research, Office of Cellular Therapies and Human Tissues, U.S. Food and Drug Administration, Silver Spring, MD, USA.
Wendell JonesIQVIA Laboratories Genomics, Durham, NC, USA.
Xian ChenDepartment of Biochemistry and Biophysics and Proteomic Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA. Electronic address: xian_chen@med.unc.edu.
Charles WangCenter for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA; Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA. Electronic address: chwang@llu.edu.

Funding

Genomic and Epigenomic Mechanisms of Maternal E-Cigarette induced Abnormal Brain DevelopmentU01DA058278 · NIDA · LOMA LINDA UNIVERSITY · PI Charles Wang, DALIAO XIAO · 2023 to 2026
$4.4M
Molecular mechanisms of CIB1 signalingR01GM133107 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CHEN, XIAN · 2019 to 2020
$617k
High Throughput DNA SequencerS10OD019960 · OD · LOMA LINDA UNIVERSITY · PI WANG, CHARLES · 2015 to 2015
$272k
NIDA NIH HHS U01 DA058278NIGMS NIH HHS R01 GM133107NIH HHS S10 OD019960
6 · The paper itself

Abstract

Next-generation sequencing requires accuracy, reproducibility, and standardized reference materials. The Sequencing Quality Control (SEQC-2) multicenter studies on paired breast cancer and B cell lines generated extensive genomic datasets, but integrated epigenomic and proteomic references remain limited. Here, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Methyl-seq, RNA sequencing (RNA-seq), and proteomic profiling to establish comprehensive multi-omics reference materials. We identified >7,700 protein groups, with 95% of genes encoding a single peptide isoform. Protein expression from CpG island (CGI)-overlapping transcripts was higher than non-CGI transcripts in both cell lines. Certain SNVs were incorporated into mutated peptides. Chromatin accessibility was regulated by CG density: CG-rich regions showed lower methylation, greater accessibility, and higher gene/protein expression, whereas CG-poor regions exhibited higher methylation, reduced accessibility, and cell line-specific expression patterns. These datasets provide well-defined genomic, epigenomic, transcriptomic, and proteomic characterizations that can serve as benchmarks for validating omics assays and bioinformatics methods, offering a valuable community resource.

Indexed as

Breast NeoplasmsEpigenomicsProteomicsTranscriptomeCell Line, TumorCpG IslandsDNA MethylationFemaleGene Expression Regulation, NeoplasticHumansMultiomicsCP: geneticsepigenomicsproteomicstranscriptomics

Identifiers

PMID41539304
PMCPMC12853167

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.