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Data and Code for “Monitoring in Real Time and Far-Red Imaging of H₂O₂ Dynamics with Subcellular Resolution”

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posted on 2025-02-04, 23:53 authored by Justin Daho LeeJustin Daho Lee, Amanda Nguyen, Chelsea E. Gibbs, Zheyu Ruby Jin, Yuxuan Wang, Aida Moghadasi, Sarah J. Wait, Hojun Choi, Kira M. Evitts, Anthony Ascencio, Samantha B Bremner, Shani Zuniga, Vedant Chavan, C. Andrew Williams, Annette Smith, Farid Moussavi-Harami, Michael Regnier, David Baker, David L Mack, Elizabeth Nance, Patrick M BoylePatrick M Boyle, Andre BerndtAndre Berndt

Description:

This dataset contains the code, data, and computational resources used to generate the results presented in the paper “Monitoring in Real-Time and Far-Red Imaging of H₂O₂ Dynamics with Subcellular Resolution.”

Contents:

  • Conda Environment – Environment configuration to ensure reproducibility.
  • Data, Visualization, and Detailed Statistics – Raw data and statistical analysis for main and supplementary figures.
  • ColabFold Prediction Structures – Computationally predicted protein structures.
  • Analysis Code for Immunofluorescence (IF) Data – Scripts for quantifying nuclear translocation.
  • Computational Cell-Scale Modeling Code – Simulations for modeling hiPSC-CMs at the cellular level.
  • This upload provides all necessary materials to reproduce the analysis and visualizations presented in the study.

For any inquiries, please contact:

Justin Daho Lee(justindaholee@gmail.com), Andre Berndt(Correspondence, berndtuw@uw.edu)

Funding

1F31DA056121-01A1

UW ISCRM Graduate Fellowship

Brain Research Foundation

UW Royalty Research Fund

UW ISCRM IPA

NIGMS R01 GM139850-01

P30 DA048736-01-Pilot

NIMH RF1MH130391

NINDS U01NS128537

NIDA R21DA051193

McKnight Foundation’s Technologies in Neuroscience Award

National Science Foundation DGE-2140004

Herbold Foundation

Biological Mechanisms of Healthy Aging Training Grant

National Institute on Aging

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NIGMS RM1 GM131981

National Institute of Arthritis and Musculoskeletal and Skin Diseases grant P30 AR074990

American Heart Association supplement grant AHA872208

BCTP- NIH – NIBIB - 5T32EB032787-02

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