PXD068742-1

PXD068742 is an original dataset announced via ProteomeXchange.

Title	Culturing of primary mouse hepatocytes is associated with major changes to the proteome and transcriptome
Description	Primary hepatocytes are a commonly used in vitro model for studying liver metabolism, but prolonged culturing results in dedifferentiation. Here we characterized the transcriptome and proteome of whole liver and primary hepatocytes as either freshly isolated cells or after 24 hours of 2D-culturing. We found that after 24 hours of 2D-culturing, hepatocytes showed differential expression of over 10,000 genes and 3,000 proteins compared to freshly isolated cells. This was accompanied by a reduced transcriptional heterogeneity and a loss of zonal markers. Cultures contained ~10% non-hepatocytes, including stellate- and dedifferentiated endothelial cells. Culturing also increased abundance of proteins associated with oxidative stress and inflammation, and changed mitochondrial, extracellular, and ribosomal protein abundance. The data generated are available in the shiny-app “Hepamorphosis”. Our finding show that primary mouse hepatocytes undergo significant changes in culture, limiting theirutility for studying physiological and molecular mechanisms related to the liver.
HostingRepository	PRIDE
AnnounceDate	2025-09-25
AnnouncementXML	Submission_2025-09-25_14:03:43.093.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ben Stocks
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-23 08:06:49	ID requested
⏵ 1	2025-09-25 14:03:43	announced

10.1097/HC9.0000000000000795;

submitter keyword: Liver, Hepatocytes, Cell Culture, Proteomics

Jonas T. Treebak
contact affiliation	Novo Nordisk Foundation Center for Basic Metabolic Research
contact email	jttreebak@sund.ku.dk
lab head
Ben Stocks
contact affiliation	University of Copenhagen
contact email	ben.stocks@sund.ku.dk
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/2025/09/PXD068742

PRIDE project URI

• PRIDE
  1. PXD068742
     1. Label: PRIDE project
     2. Name: Culturing of primary mouse hepatocytes is associated with major changes to the proteome and transcriptome