Distinct changes to hippocampal and medial entorhinal circuits emerge across the progression of cognitive deficits in epilepsy

Yu Feng1, Keziah S. Diego1, Zhe Dong1, Zoé Christenson Wick1, Lucia Page-Harley1, Veronica Page-Harley1, Julia Schnipper1, Sophia I. Lamsifer1, Zachary T. Pennington1, Lauren M. Vetere1, Paul A. Philipsberg1, Ivan Soler1, Albert Jurkowski1, Christin J. Rosado1, Nadia N. Khan1, Denise J. Cai1, Tristan Shuman1

1: Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai

##Original code developed for the publication

Data and Analysis

All data and analysis are available here for reproduction and further analysis.

Data Access

Data, including all LFP and spike data, is available online on the DANDI Archive (https://dandiarchive.org; dataset #000638).

Analysis files

All analysis were conducted using MATLAB, Python,and Prism.

Each main folder contains analysis files used for the given figure.

A brief description of each file is provided below.

Figures

Preprocessing

EphysProcessingPipelineSF_Preprocessing (.m)
Organized animal experient info in a folder
Called_functions: contains all called functions and scripts within the main MATLAB script

Figure 1

Fig1CDEF_Prism file for NOL behavior (PRISM)

Figure 2

Fig2D_example LFP trace plotting code (.m)
Fig2B_Seizure count prism file (PRISM)
Called_functions: contains all called functions and scripts within the main MATLAB script

Figure 3

Fig3AB_HPC coherence and power code (.m)
Fig3B_Coherence plotting code in Python (.py in folder)
Fig3CD_Phase locking of DG inhibitory cell to CA1 (mu and r) (.m)
Fig3E_Firing rate of DG inhibitory cells (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Figure 4

Fig4ADBE_ Phase locking of MEC2 and MEC3 excitatory cells to HPC theta (mu and r) (.m)
Fig4CF_Firing rate of MEC2 and MEC3 excitatory cells (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Figure 5

Fig5A_Plotting code for MEC3 subclusters (.m)
Fig5A_MEC3 subcluster relative to shank location plotting (.m)
Fig5BECF_ Phase locking of MEC3 Trough and Peak-locked excitatory cells to HPC theta (mu and r) (.m)
Fig5DG_ Firing rate of MEC3 Trough and Peak-locked excitatory cells (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Figure 6

Fig6AB_HPC and MEC Coherence code (.m)
Fig6AB_Coherence plotting code in Python (.py in folder)
Called_functions: contains all called functions and scripts within the main MATLAB script

Figure 7

Fig7AB_Coherence subsampling code (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Supp Figure 4

SuppFig4A_Speed output csv (.CSV)
SuppFig4A_Speed output Prism file (PRISM)
SuppFig4BC_Power and coherence code from MATLAB (.m)
SuppFig4C_Coherence plotting code in Python (.py)

Supp Figure 5

SuppFig5A_H_Output coherence and power (.m)
SuppFig5A-H_organized seizure information during silicon probe recording and during EEG recording (.CSV)
SuppFig5A-H_Prism plotting (PRISM)
Called_functions: contains all called functions and scripts within the main MATLAB script

Supp Figure 6

SuppFig6A-F_IED detection code (.m)
SuppFig6A-F_prism file of correlation between IED and coherence and power (PRISM)
Called_functions: contains all called functions and scripts within the main MATLAB script

Supp Figure 7

SuppFig7AB_HPC and MEC exc and inh clustering plot (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Supp Figure 8

SuppFig8ABDE_MEC2/3 inhibitory cell phase locking mu and r (.m)
SuppFig8CF_Firing rate of MEC2/3 inhibitory cells (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Supp Figure 9

SuppFig9A_example waveform plot for Trough and Peak-locked units (.m)
SuppFig9BCDEF_firing properties of MEC3 Trough and Peak-locked units (.m)
SuppFig9BCDEF_prism file of firing properties of MEC3 Trough and Peak-locked units (PRISM)
SuppFig9GH_MEC3 subclusters hard-cutoff (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

Supp Figure 10

SuppFig10B_code for the percentage of subsampled bins (.m)
SuppFig10C_Proportion of subsampled bins during run and run-initiation
SuppFig10D_python code for the proportion of subsampled bins across the track (.py in folder)
SuppFig10E_running speed during subsampled bins (.m)
Called_functions: contains all called functions and scripts within the main MATLAB script

ShumanLab/Feng_CellReports