Data for: A Morphology-Based Machine Learning Model for Scoring Epithelial-Mesenchymal Plasticity using Organelle Dynamics
type: Dataset
description: Project Description: This project is aimed at modelling dynamic organelle morphology changes in a cellular model of epithelial-mesenchymal transition (EMT). EMT is a developmental process, which is re-activated in cancer and promotes invasion, metastasis and resistance to various therapies. The repository contains raw microscopy images (.nd2 files) and numerical data outputs of all the experiments performed on a variety of cell lines (breast cancer, lung cancer). Cells were stained with the CellPainting kit. Experiments codes are listed below. Categories: Translational and applied bioinformatics; Cellular interactions (incl. adhesion, matrix, cell wall) Numerical Data Source_wet lab + database (782.78 KB) (1 excel file with numerical data source for MS experiments; 1 pdf file with WB uncropped membranes images) Numerical Source Data_all CP experiments (microscopy): (14.47 GB) - CP015/016/018: NMuMG training set (cellprofiler outputs) - CP017: NMuMG reversal experiment - CP019:NMuMG model validation - CP020: breast cancer cells - CP_INT_03_Normoxia: A549 Normoxia - CP_INT_03_Hypoxia: A549 Hypoxia Images (.ND2 files): - CP015_nd2 (37.24 GB): NMuMG training set.1 - CP016_nd2 (37.24 GB): NMuMG training set.2 - CP018_nd2 (37.24 GB): NMuMG training set.3 - CP017_nd2 (37.24 GB): NMuMG reversal experiment - CP019_nd2 (37.24 GB): NMuMG model validation - CP020_nd2 (37.24 GB): breast cancer cells - CP_INT_03_Normoxia_nd2 (18.62 GB): A549 Normoxia - CP_INT_03_Hypoxia_nd2 (18.62 GB): A549 Hypoxia Image files are in nd2 format, which is Nikon's proprietary format, but can be viewed with open source tools such as ImageJ.
conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
conditions of access: info:eu-repo/semantics/openAccess
contributor: Justin Slager
contributor: Francesca Gatto
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Jonas Fuxe
date modified: 2025-11-24
date published: 2025-11-24
funding: Grant
  identifier: 21 1739 Pj; 24 3842 Pj
  funder: Swedish Cancer Society
funding: Grant
  identifier: 211092; 231172
  funder: Radium Hemmets Research Funds
language: English
is part of: https://doi.org/10.48723/8wk0-kt27
keywords: Cell and Molecular Biology
keywords: Basic Cancer Research
keywords: Organelle Shape
keywords: Epithelial-Mesenchymal Transition
keywords: Triple Negative Breast Neoplasms
keywords: Cell Plasticity
keywords: Triple-negative breast cancer
publisher: Karolinska Institutet
spatial coverage: Sweden
temporal coverage: 2023-09-01/2025-12-01
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version: 1

PropertyValue
property ID: DOI
value: 10.48723/m1cg-v223

Justin Slager
type: Person
affiliation: Karolinska Institutet
family name: Slager
given name: Justin

Karolinska Institutet
type: Organization
department: Department of Laboratory Medicine

Francesca Gatto
type: Person
affiliation: Karolinska Institutet
family name: Gatto
given name: Francesca

Jonas Fuxe
type: Person
affiliation: Karolinska Institutet
family name: Fuxe
given name: Jonas

Swedish Cancer Society
type: Organization

Radium Hemmets Research Funds
type: Organization

English
type: Language
alternate name: eng

Sweden
type: Place

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