Study Overview

This dataset is from: "Diethorn, E. J., Rathaur, A. B., Ruiz Lopez, B. R., Eke, C., & Gould, E. (2026). Developmental CA2 perineuronal net reduction restores social memory in Shank3 mutant mice. Communications Biology."

Access this dataset on Dryad: DOI 10.5061/dryad.wm37pvn2t

This study investigated how atypical development of perineuronal nets (PNNs) in hippocampal area CA2 contributes to impaired emergence of developmental social recognition abilities in Shank3B knockout (KO) mice.

Contents

This READ ME file includes the following information:

1. Acronyms and abbreviations
2. Explanation of files in the repository
3. Data acquisition parameters
4. Electrophysiology and codes
5. Animal information by figure
6. Confocal imaging settings and analysis notes
7. Research Resource Identification Numbers (RRIDs)
8. Other software
9. List of variables

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1. Acronyms and Abbreviations

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2. Explanation of Files

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3. Data Acquisition Parameters

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4. Electrophysiology and Codes

Description of Files

Ephys_RawData: Contains Matlab files, 1 for each recording session: pre-social ('Baseline'), novel, post-social ('Homecage'), and familiar. Each .mat file contains 1 variable per animal, using the following naming conventions:

• For the baseline experiment (Fig. 2, S2, S3): Animal origin_ID number_Cohort_Trial
• For the chABC experiment (Fig. 5, S8): Treatment_Animal origin_ID number_Cohort_Trial

Within each variable is a matrix containing the following data:

• Column 0 = Timestamp, in milliseconds
• Columns 1-4 = Electrophysiological data from each recording channel, in millivolts
• Note that some animals have fewer than 4 electrodes, as any electrode not in a CA2 layer was excluded

Ephys_Behavior_Epochs: Contains Matlab files, 2 for the novel and familiar recording sessions (immobility epochs and social investigation epochs) or 1 for pre- and post-social recording sessions (immobility epochs). Each .mat The file contains 1 variable for each animal, named identically to the corresponding variable in the LFP file (above). Within each variable is a matrix containing the following data:

• Column 0 = Bout start time in milliseconds
• Column 1 = Bout end time in milliseconds
• Each row is therefore a separate behavioral epoch

Recording Parameters

Code Information

Availability: Custom Python codes can be accessed at the following DOI: 10.5281/zenodo.19476011

Overview: This repository contains 6 Python scripts for analyzing local field potential (LFP) recordings from multi-electrode arrays. The pipeline covers three analyses — sharp-wave ripple (SWR) detection, spectral power, and aperiodic component estimation — each available in two variants: across the full trial or restricted to specific behavioral bouts (behavior-locked).

Input/Output: All scripts read MATLAB .mat files as input and write results to Excel workbooks (.xlsx).

Software and dependencies: All scripts were written and tested in Python 3. The following packages are required:

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5. Animal Information by Figure

All source data included in these figures can be found in the corresponding spreadsheet entitled "Diethorn et al., 2026_Figure Data".

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6. Confocal Imaging Settings & Analysis Notes

Imaging Settings

Note: Analyzed channels are shown in bold.

Figure-Specific Analysis Notes

Note: All images taken with 1024 x 1024 resolution. Raw, coded .lif confocal files are available to download from the Dryad repository for each analysis. Decoded animal information can be found in the corresponding spreadsheet entitled "Diethorn et al., 2026_Decoded Confocal Files".

Note: c-fos in the CA2 was counted manually in figures 2c and 5b, so there are no corresponding confocal images.

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7. Research Resource Identification Numbers (RRIDs)

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8. Other Software

• ANY-maze (v7.43) was used to track animal position in the P60 object location videos with the goal of assessing locomotive differences between adult KO and WT mice. The X and Y positions from these videos have been uploaded as a .zip file to this repository.
• NeuroExplorer (v5.306) was used to downsample raw LFP data collected using a Plexon Omniplex system and export data to Matlab.
• Matlab (vR2024b) was used to export and store electrophysiology-related data.
• Python (v3) was used to analyze electrophysiological data using the .mat files derived from NeuroExplorer.
• Avisoft RECORDER (v4.2.29) software was used to record USVs using a single microphone.
• Avisoft SASLab Pro (v5.2.13) software was used to generate spectrograms from .wav files and conduct semi-automated analysis of USVs.
• Graphpad Prism (v10.6.0) was used for statistical analysis and generating plots and figures.
• BORIS (v7.13.9) was used to manually annotate behavioral videos collected during electrophysiology recording sessions. These manual annotations collected epochs of immobility as well as of active investigation, both of which are included in this repository.
• Fiji (Image J) was used to conduct analyses of confocal images and to prepare images for figure display.

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9. List of Variables

Explanation of dependent variables that appear in the main and supplementary figures.