DLC1 knockdown in EMT in MCF10A cells

Version 1.0
Höpfl, Sebastian; Radde, Nicole, 2025, "DLC1 knockdown in EMT in MCF10A cells", https://doi.org/10.18419/DARUS-4240, DaRUS, V1
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Description

MCF10A cells were seeded and transfected with two siRNAs targeting dlc1 and one control siRNA. 10 ng/ml TGFb was used to induce EMT and added 24 h after the transfection.

For modeling, the CBS model of Tian et al. (2003) was extended by DLC1. The model was calibrated using the MCF10A data after 5 days under the control and dlc1 targeted siRNA.
The Repository contains:
- The CBSD model in the SBML format
- A PEtab problem describing the parameter estimation problem (experimental data, observables, parameters, experimental conditions)
- Script used for model calibration (Extended_CBS_Pypesto_ParEst.py)
- Script used for MCMC sampling (MCMC_sampling_pypesto_workflow.py)
- Jupyter notebook used for model simulation (Extended_CBS_SNAIL1_libRoadRunner_simulation.ipynb)
- Jupyter notebook used for bifurcation analysis(Bifurcation_Extended_CBS_SNAIL1_PyDSTool.ipynb)
- The MCMC sampling results in HDF5
- Created Visualisations
- The results of the full CBSD model (with all parameters = before model reduction)
- code used in Fiji for the segmentation and analysis of the IF data (get_boundaries_v9.ijm)
Subject Medicine, Health and Life Sciences
Keyword DLC1, EMT, Deleted in Liver Cancer 1, Epithelial to Mesenchymal Transition
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all_parameters_estimated.zip
ZIP Archive - 28.3 MB
Published Mar 21, 2025
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MD5: 76a0ba8b915781461f0ec37570945ea6
Model calibration and MCMC results of the not reduced CBSD model
Preview "all_parameters_estimated.zip"
Bifurcation_analysis.zip
ZIP Archive - 13.8 MB
Published Mar 21, 2025
1 Download
MD5: 80a109261dea1a57bc7bc1236f4fe887
Skripts to perform the Bifurcation analysis using PyDSTools
Preview "Bifurcation_analysis.zip"
CBSD_global_parameter_variation_RACIPE.py
Python Source Code - 17.3 KB
Published Mar 21, 2025
1 Download
MD5: 6f7f286f961b2490fc107539b2baec56
Script for the modified RACIPE analysis of the CBSD model
CBSD_libRoadRunner_simulation.ipynb
Jupyter Notebook - 6.4 MB
Published Mar 21, 2025
1 Download
MD5: d59fd8cdae24a08a96ddfc3e3bc3469d
Jupyter notebook for deterministic and stochastic CBSD simulation
CBSD_MCMC_chain.hdf5
Hierarchical Data Format - 122.1 MB
Published Mar 21, 2025
2 Downloads
MD5: 452f4f6ede41fc70fcdc0184d9c3ebfc
Complete posterior samples from MCMC sampling in HDF5
Preview "CBSD_MCMC_chain.hdf5"
CBSD_PEtab.zip
ZIP Archive - 6.5 KB
Published Mar 21, 2025
1 Download
MD5: 263e316228d02aa4da0c4476ba2c06d6
PEtab files for the CBSD model including the CBSD SBML model. Can be used to reproduce the parameter estimation, simulation and sampling.
Preview "CBSD_PEtab.zip"
CBSD_Pypesto_Parameters.hdf5
Hierarchical Data Format - 118.4 KB
Published Mar 21, 2025
1 Download
MD5: 7a5b0997d318069f5aeb7ced5d66cd10
Model calibration results in HFD5 format
Preview "CBSD_Pypesto_Parameters.hdf5"
CBSD_Pypesto_Parameters_optimization_dictionary.json
JSON - 931 B
Published Mar 21, 2025
1 Download
MD5: b79c3cfb6b6ab7ceda22fd319c5337db
Dictionary containing the optimized parameter values
CBSD_single_reactions_SSA.xml
XML - 34.5 KB
Published Mar 21, 2025
1 Download
MD5: ee6c89ff248f53a6cbb07eabfef12fa7
SBML CBSD model for stochastic simulations - models all subreactions individually
get_boundaries_v9.ijm
Unknown - 12.1 KB
Published Mar 21, 2025
1 Download
MD5: e1a4c3d561bd5afb7abdf253deb07962
Script used for the IF images segmentation and analysis for classification into E-cad and N-Cad positive cells
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