PXD024353

PXD024353 is an original dataset announced via ProteomeXchange.

Title	Proteomic characterisation of inducible proteins in three dimensional cultures
Description	Three-dimensional models have gained significant traction over the past decade and are considered a powerful tool for improving the concordance between in vitro and in vivo phenotypes. However, the duration of spheroid culture may influence the degree of correlation between these counterparts. When using immortalised cell lines as model systems, the assumption for consistency and reproducibility is often made without adequate characterization or validation. It is thus essential to investigate the proteomic dynamics of each spheroid model, which arises due to culture duration, to define their biology most appropriately. As an example, we assessed the influence of culture duration on the relative proteome abundance of HepG2 cells cultured as spheroids, which are routinely used to model the liver. Quantitative proteomic profiling of whole cell lysates labelled with tandem-mass tags was conducted using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In excess of 4800 proteins were confidently identified, which were shared across three consecutive time points over 28 days. The HepG2 spheroid proteome was divergent from the monolayer proteome after 14 days in culture and continued to change over the successive culture time points. Proteins representing the recognised core hepatic proteome, cell junction, extracellular matrix, and cell adhesion proteins were extensively modulated.
HostingRepository	PRIDE
AnnounceDate	2021-05-26
AnnouncementXML	Submission_2021-05-25_22:21:51.442.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024353
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andrea Ellero
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-24 04:09:03	ID requested
⏵ 1	2021-05-25 22:21:51	announced

Dataset with its publication pending

submitter keyword: HepG2, Spheroids, Proteomics

Alan Duncan Cromarty
contact affiliation	Department of Pharmacology Faculty of Health Sciences School of Medicine University of Pretoria
contact email	duncan.cromarty@up.ac.za
lab head
Andrea Ellero
contact affiliation	University of Pretoria
contact email	u13209656@tuks.co.za
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/2021/05/PXD024353

PRIDE project URI

• PRIDE
  1. PXD024353
     1. Label: PRIDE project
     2. Name: Proteomic characterisation of inducible proteins in three dimensional cultures