Matlab Codes for Forero2020

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Repository for all modelling data and associated MATLAB codes for

Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene

https://www.biorxiv.org/content/10.1101/2020.04.03.024414v1 [link to accepted paper]

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Data files

• ./Data_files
  • Nasc_TranscriptsCount - mRNA fish quant counts
  • Raw_Intensities Analysis-BLC_W_BG_RunAve_May18 - Correlation Data with running average
  • Raw_Intensities Analysis-BLC_W_BG_WO_RunAve_May18 - Raw Correlation Data
  • RawCorrelationsData - 6 correlations seperated into sheets
  • Renor_aligned_TPLData - aligned triptolide data
  • sub_1_min_data - Correlations from .15s frame rate movies

Model Objects

./Model_files

• SimpleModel.m - Best fit (chosen) model object file
• TwoS_BurstingModel.m - Two state bursting model
• RNAP_SER5_SplitModel.m - Phosphorylation model
• mRNAsoloModel.m - mRNA retention model
• GenericModel.m - generic model obj

Model Fits

• ./Model_fits
  • Simple_MH_results
    • 3.17.2021 - Primary model fit and MCMC chains (Chains E)

GUI

• TranscriptionModel.mlapp