Transient pores account for cell-penetrating peptides and homeoproteins translocation

---
title: README
author: Hugues BERRY
---

# Synopsis
This repository provides access to the experimental data used in the article :

Trofimenko, E., Gervasi, N., Perez, S., Rodriguez, N., Ravault, D., Cribier, S., Berry, H., Venance, L. and Sagan, S., (2026). Transient pores account for cell-penetrating peptides and homeoproteins translocation, accepted in the *Proceedings of the National Academy of Sciences of the United States of America*

The data consists in patch-clamp recordings of different cell types (CHO-K1, A745 etc) in presence of various concentrations and types of cell-penetrating peptides / CPPs (R9, RL9, RW9 etc...)

# Directory organization
- The repository is organized into 5 directories:
	- A745: experiments in CHO-psgA-745 cells
	- CHO-K1: experiments in CHO-K1 cells
	- CHO-K1_LT_11C: experiments i CHO-K1 cells at 11°C (fig S4)
	- SKoV: experiments in SKOV3 cells
	- Slides: experiments in acute brain slices (fig 5)

- Each directory in turn contains directories corresponding to the CPP used, that can be, depending on the cell type: 
	- cargo (ie KRAKLAK), 
	- EN2, 
	- OTX2, 
	- Penetratin
	- R6L3, 
	- R6W3, 
	- R6W3-cargo (ie R6W3-KRAKLAK), 
	- R10W6 (fig S3). 
	- R9, 
	- TAT, 
	- The 'NT' directory corresponds to control experiments, without CPP

# Data organization
Each CPP directory contains a single Matlab binary data file: xpdata.mat that can be open in Matlab using the "load" command (or by double-clicking on the .mat file).  

The file contains a struct array with one struct per experiment (a current sweep). Each experiment is a struct with 17 fields:
- *conc*: CPP concentration (in µM)
- *trial*: cell id (there are several sweeps per cell)
- *sweepn*: sweep number in this cell
- *dt*: sampling interval for the patch-clamp recording (in ms)
- *CPP*: name of the CPP
- *V*: holding potential (in mV)
- *I*: current recording / trace (in pA) 
- *nevents*: number of transient current events detected in the current trace
- *meandur*: mean duration of the events of the current trace (in ms)
- *meanampl*: mean amplitude of the events of the current trace (in pA)
- *stdbase*: event threshold  of the current trace (see Material & Methods)
- *amplitudes*: individual mean amplitude of each transient event  of the current trace 
- *bayes*: a struct storing the result of the Bayesian analysis for pon and poff, with 4 fields:
	- *allrates*: a 2x4001 vector giving the successive estimations of pon (row 1) and pof (row2) at each iteration of the Bayesian inference
	- *burnin*: the length of the iteration windows that is to be skipped to compute the posterior from allrates
	- *alllogfitness*: a vector giving the log of the fitness at each iteration of the Bayesian inference
	- *delta*: max amplitude of the MH sampling proposal variants (cf Siekman, Sneyd and Crampin. 2012. Biophys J 103:2275-2286)
- *E*: the segmented current trace where each time point of I is 1 if the time point belongs to a current event, 0 otherwise
- *baselineampl*: mean amplitude (in pA) of each current event (above its baseline)
- *nswitches*: number of switches between open and close states in the experiment
- *sumcharges*: total charge transfer for all the events in the experiment