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.
citation: CreativeWork
  name: Fuxe, J., Slager, J., Gatto, F., Frey, B., Porebski, B., Carreras-Puigvert, J., Parniewska, M., & Shi, W. (2025). A Morphology-Based Machine Learning Model for Scoring Epithelial-Mesenchymal Plasticity using Organelle Dynamics. In Research Square. https://doi.org/10.21203/rs.3.rs-5859608/v1
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: 2026-03-05
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
  type: DefinedTerm
  term code: 30108
keywords: Medical Bioinformatics and Systems Biology
  type: DefinedTerm
  term code: 30113
keywords: Basic Cancer Research
  type: DefinedTerm
  term code: 30112
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

PropertyValue
property ID: DOI
value: 10.21203/rs.3.rs-5859608/v1

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

Organelle Shape
type: DefinedTerm
description: The quality of surface form or outline of ORGANELLES.
term code: D053140

Epithelial-Mesenchymal Transition
type: DefinedTerm
description: Phenotypic changes of EPITHELIAL CELLS to MESENCHYME type, which increase cell mobility critical in many developmental processes such as NEURAL TUBE development. NEOPLASM METASTASIS and DISEASE PROGRESSION may also induce this transition.
term code: D058750

Triple Negative Breast Neoplasms
type: DefinedTerm
description: Breast neoplasms that do not express ESTROGEN RECEPTORS; PROGESTERONE RECEPTORS; and do not overexpress the NEU RECEPTOR/HER-2 PROTO-ONCOGENE PROTEIN.
term code: D064726

Cell Plasticity
type: DefinedTerm
description: The ability of a cell to change its PHENOTYPE in response to changes in the environment.
term code: D000066670

Triple-negative breast cancer
type: DefinedTerm
description: Triple negative malignant neoplasm of breast (disorder)
term code: 706970001

Sweden
type: Place

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