DLC1 knockdown in EMT in MCF10A cells

<p>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.</p>

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.
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The Repository contains:
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- The CBSD model in the SBML format<br>
- A PEtab problem describing the parameter estimation problem (experimental data, observables, parameters, experimental conditions)<br>
- Script used for model calibration (Extended_CBS_Pypesto_ParEst.py)<br>
- Script used for MCMC sampling (MCMC_sampling_pypesto_workflow.py)<br>
- Jupyter notebook used for model simulation (Extended_CBS_SNAIL1_libRoadRunner_simulation.ipynb)<br>
- Jupyter notebook used for bifurcation analysis(Bifurcation_Extended_CBS_SNAIL1_PyDSTool.ipynb)<br>
- The MCMC sampling results in HDF5<br>
- Created Visualisations<br>
- The results of the full CBSD model (with all parameters = before model reduction)
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- code used in Fiji for the segmentation and analysis of the IF data (get_boundaries_v9.ijm)