ripples_emergence_inhibition/README.md

A developmental increase of inhibition promotes the emergence of hippocampal ripples

Irina Pochinok, Tristan M. Stöber, Jochen Triesch, Mattia Chini, Ileana L. Hanganu-Opatz

Preprint on biorxiv (here).

The repository contains in vivo single unit activity (SUA) and local field potential (LFP) data recorded from the hippocampal CA1 area (HP) and the medial prefrontal cortex (mPFC) of developing mice (4-12 postnatal days).

The data is split into four folders based on the type of an experiment:

1. baseline: spontaneous activity (P4-12 mice, 111 mice).
2. optogenetic: optogenetic stimulation of PYRs in the CA1 area (P8-12 mice, 27 mice).
3. chemogenetic: chemogenetic silencing of INs in the CA1 area (P11-12 mice, 15 mice).
4. movement_controls: spontaneous activity with video tracking (P11-12 mice, 7 mice).

All folders include dataset_info.csv file with mice information. Opto dataset includes a description of stimulation protocol (opto_stim_protocol.txt) and file with stimulation periods (stim_periods_control_group.txt and stim_periods_opsin_group.txt). Movement_controls dataset includes a configuration files for video frames and ephys data alignment (movement_ephys_alignment).

Electrode geometry

The HP data has been recorded using a laminar probe, with 50 micrometers between channels. For both LFP and SUA data from 7 channels are given: channel 4 corresponds to the channel with LFP signal "reversal" observed in the stratum pyramidale, channels 1:3 are above and channels 5:7 are below.

The PFC data has been recorded using a 4x4 4-shank probe, with 100 micrometers of spacing between recording sites on the same shank and 125 micrometers between shanks. Channels 1-4 are on the most medial shank, channels 13-16 are on the most lateral shank, channels 1-5-9-16 are the most dorsal ones, and channels 4-8-12-16 are the most ventral ones.

LFP

LFP data is provided as .mat files, file name starts with the dataset unique animal_id. Each .mat file contains 2d array, n_channels x n_timepoints. The sampling frequency is 1000Hz.

SUA

SUA data is provided as .mat files, file name starts with the dataset unique animal_id. Each .mat file contains a structure with spiking data. The spike timepoints are in sampling frequency 32kHz.

For every question and/or further data request, please don't hesitate in contacting me (irina.pochinok@zmnh.uni-hamburg.de or i.pochinok@gmail.com).