Datasets and scripts presented in "Long-term in vivo application of a potassium channel-based optogenetic silencer in the healthy and epileptic mouse hippocampus" (Kleis et al., submitted to BMC Biology in 2021)

Piret Kleis a2168cecb5 'datacite.yml' ändern 2 years ago
DATA-KA 7ffefa2692 Dateien hochladen nach '' 2 years ago
DATA-Sal-PACK 9f90a3141a Dateien hochladen nach 'DATA-Sal-PACK' 2 years ago
DATA-Sal-bPAC 16b32b943f Dateien hochladen nach '' 2 years ago
DATA_KA-PACK 98829a054a Dateien hochladen nach '' 2 years ago
DATA_KA-bPAC 7889601cca Dateien hochladen nach '' 2 years ago
DATA_Sal f826090b01 Dateien hochladen nach '' 2 years ago
DATA_Sal_mCherry 330761d8fc Dateien hochladen nach '' 2 years ago
LFP_nomenclature_and_datasets.xlsx ec8ae95d7d Dateien hochladen nach '' 2 years ago
LICENSE 6b1ff87fc1 Initial commit 2 years ago
README.md 7093faefcf 'README.md' ändern 2 years ago
datacite.yml a2168cecb5 'datacite.yml' ändern 2 years ago
script1_line-length_analysis.py e66b38be7f 'script1_line-length_analysis.py' ändern 2 years ago
script2_linelengths_of_snippets_Fig2.py 2956de132c 'script2_linelengths_of_snippets_Fig2.py' ändern 2 years ago
script3_spectral_analysis.py 1d728f8d97 'script3_spectral_analysis.py' ändern 2 years ago

README.md

Long-term in vivo application of a potassium channel-based optogenetic silencer in the healthy and epileptic mouse hippocampus

Here we provide the electrophysiological datasets and Python scripts, which underlie the data analysis and conclusions in our paper about the novel potassium channel-based optogenetic silencer, PACK, and its application in vivo (Kleis et al., submitted to BMC Biology in 2021). We recorded local field potentials (LFPs) with wire electrodes, which were chronically implanted into the hippocampus of healthy or non-epileptic adult male mice. The LFPs were acquired from freely behaving mice, which were placed into the recording arena for three hours either without illumination (reference recording) or with an optogenetic stimulation (at 0.05 Hz or 0.1 Hz) during the second hour. We had six experimental groups, which are presented in the file named "LFP_nomenclature_and_datasets.xlsx". Further details about the experimental groups and methods are presented in the published article.

The datasets contain LFPs resampled at 500 Hz in .h5 file format. We uploaded LFPs acquired at the contralateral hippocampal electrode ('HCc') of the non-epileptic mice (saline-injected groups). For epileptic mice (kainate-injected groups), data from ipsilateral ('HCi') and contralateral hippocampal electrodes are presented.

The Python codes that were used to analyze the data and generate the figures can be found in three scripts:

Script 1: contains the function for calculating line length. Script 1 was used to generate subfigures in Fig.1, Fig. 4, Fig.S2, Fig. S3, and Fig. S4.

Script 2: contains functions for (1) extracting data snippets before and after light pulses and (2) calculating line length for these snippets. Additionally, examples are provided of how we used the functions (3) to extract LFP snippets and save them as matrices and (4) to calculate and save the line lengths of these snippets. Script 2 was used for Fig. 2.

Script 3: contains functions for spectral analysis, including calculation and plotting of power spectral density (PSD) and plotting of spectrograms. The script contains three examples of how the functions were used to analyze and present data.

Example 1. Plotting individual PSDs and creating a matrix with all PSDs

Example 2. Extracting the power areas of the delta, theta, beta, and gamma oscillations by calculating the area under the curve of PSD plots in respective ranges

Example 3. Plotting spectrograms

The script 3 was used for Fig. 3, Fig. 4, Fig. S2, and Fig S3.

datacite.yml
Title Long-term in vivo application of a potassium channel-based optogenetic silencer in the healthy and epileptic mouse hippocampus
Authors Kleis,Piret;Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany;ORCID:0000-0001-9247-8842
Paschen,Enya;Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany;ORCID:0000-0001-6323-3889
Häussler,Ute;Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany;ORCID:0000-0001-5601-9833
Bernal Sierra,Yinth Andrea;Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
Haas,Carola;Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, 79106, Freiburg, Germany
Description Here we provide the electrophysiological datasets and Python scripts, which underlie the conclusions in our paper about application of the novel potassium channel-based optogenetic silencer, PACK, in vivo (Kleis et al., 2021, preprint in BioRxiv and submitted publication in BMC Biology). We recorded the local field potentials (LFPs, resampled at 500 Hz, uploaded in .h5 format) with wire electrodes, which were chronically implanted into the hippocampus of freely behaving healthy or non-epileptic adult male mice. The six experimental groups are named in LFP_nomenclature_and_datasets.xlsx with further details in the published article. The Python scripts contain functions for calculating and plotting line length, power spectral density, and spectrograms.
License Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References Kleis, P., Paschen, E., Haeussler, U., Sierra, Y.A.B. and Haas, C.A., 2021. In vivo characterization and application of a novel potassium channel-based optogenetic silencer in the healthy and epileptic mouse hippocampus. bioRxiv. [https://doi.org/10.1101/2021.09.06.459077 ] (IsSupplementTo)
Funding DFG, HA 1443/11-1
DFG, SPP1926
Keywords bPAC
cyclic AMP
Electrophysiology
Epilepsy
Hippocampus
Kainate
Neuroscience
Optogenetic inhibition
Potassium
Resource Type Dataset