This repository contains all data, code and figures for the papers "Rapid characterisation of hERG channel kinetics I: using an automated high-throughput system" and "Rapid characterisation of hERG channel kinetics II: temperature dependence".
room-temperature-only: Results of "Rapid characterisation of hERG channel kinetics I: using an automated high-throughput system".
temperature-dependency: Results of "Rapid characterisation of hERG channel kinetics II: temperature dependence". The hierarchical Bayesian mean model for 37°C is also available as a CellML file.
syn-room-temperature-only: Synthetic data studies supporting "Rapid characterisation of hERG channel kinetics I: using an automated high-throughput system".
The code requires Python 2.7 and two dependencies: PINTS and Myokit. Matplotlib is required to regenerate the figures, and one of the figures also requires Seaborn.
data: Contains all .csv type data exported from automated QCs (see qc). Each protocol for each cell is saved as a separate file, currents are stored in the unit of [picoampere]. Time points for the current trace is saved as a separate file (to reduce duplicated information), and are in the unit of [second].
data-sweep2: Same as data, but exporting second sweep of the recorded data, currently for staircaseramp protocol only.
data-autoLC: Same as data, but using automated leak correction done by Nanion SynchoPatch384PE. Mainly for non-staircase ramp protocols, as we do not have an explicit leak estimation step in all of our protocols except staircase-ramp, and we hope their automated leak correction can do a better job if leak changes between protocols.
data-raw: Same as data, but with raw data without any post-processing, contains *-before.csv and *-after.csv, referring to before and after E-4031 addition respectively; currently only contain herg25oc1-staircaseramp data.
lib: Contains all external Python libraries (require manual installation, see README) and other modules/utility functions.
mmt-model-files: Myokit model files, contains IKr model.
protocol-time-series: Contains protocols as time series, stored as .csv files, with time points (in [second]) and voltage (in [millivolt]).
qc: Contains QC information for the selected cells in data, obtained using automated QC hergqc.py.
supplement-info: Contains extra information/tables for the Supporting Materials.
If you publish any work based on the contents of this repository please cite:
Lei, C. L., Clerx, M., Gavaghan, D. J., Polonchuk, L., Mirams, G. R., Wang, K. (2019). Rapid characterisation of hERG channel kinetics I: using an automated high-throughput system. Biophysical Journal, 117, 2438-2454.
Lei, C. L., Clerx, M., Beattie, K. A., Melgari, D., Hancox, J., Gavaghan, D. J., Polonchuk, L., Wang, K., Mirams, G. R. (2019). Rapid characterisation of hERG channel kinetics II: temperature dependence. Biophysical Journal, 117, 2455-2470.