Data from: Scn2a insufficiency alters spontaneous neuronal Ca2+ activity in somatosensory cortex during wakefulness
Data files
Oct 04, 2023 version files 2.64 MB
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Behavioral.xlsx
12.74 KB
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CaImaging.xlsx
1.97 MB
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ECoG.xlsx
11.75 KB
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qPCR.xlsx
14.48 KB
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README.md
3.30 KB
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WesternBlot.zip
628.93 KB
Abstract
SCN2A protein-truncating variants (PTV) can result in neurological disorders such as autism spectrum disorder and intellectual disability, but they are less likely to cause epilepsy in comparison to missense variants. While in vitro studies showed PTV reduce action potential firing, consequences at in vivo network level remain elusive. Here, we generated a mouse model of Scn2a insufficiency using antisense oligonucleotides (Scn2a ASO mice), which recapitulated key clinical feature of SCN2A PTV disorders. Simultaneous two-photon Ca2+ imaging and electrocorticography (ECoG) in awake mice showed that spontaneous Ca2+ transients in somatosensory cortical neurons, as well as their pairwise co-activities were generally decreased in Scn2a ASO mice during spontaneous awake state and induced seizure state. The reduction of neuronal activities and paired co-activity are mechanisms associated with motor, social and cognitive deficits observed in our mouse model of severe Scn2a insufficiency, indicating these are likely mechanisms driving SCN2A PTV pathology.
README
Scn2a insufficiency alters spontaneous neuronal Ca2+ activity in somatosensory cortex during wakefulness
https://doi.org/10.5061/dryad.83bk3j9z2
Data used to determine the molecular expression, behavioral phenotype, ECoG and in vivo two-photon calcium imaging activities in mouse model of Scn2a insufficiency and in control mice. Folder also includes the customized MATLAB script used for in vivo imaging analysis.
File structure and data description
qPCR.xlsx -- qPCR data on Scn2a mRNA expression (Ct values and % change compared to control)
WesterBlot.zip -- Western Blot data on Scn2a protein expression
- Gapdh.jpg -- Image of the reference protein bands, left 3 lanes are control and right 3 lanes are Scn2a ASO treated
- Scn2a.jpg -- Image of the Scn2a protein bands, left 3 lanes are control and right 3 lanes are Scn2a ASO treated
- WesternBlotAnalysis.xlsx -- Band intensities calculations (% change compared to control). Colored cells are the finalized values reported in Figure 1B of manuscript
Behavioral.xlsx -- data showing %duration in 3-chamber, elevated plus maze and open field. Also contains nesting score.
CaImaging.xlsx --calcium transients events data: mean amplitude (ampl, dF/F), frequency (freq, events/sec), normalized integral (normint) and pairwise correlation (averaged similarity index). Genotype where 0 = control, 1 = ASO treated mice. Drug where 0 = baseline, 1 = after PTZ. File also shows statistical summary from linear mixed effect model of each parameter.
ECoG.xlsx -- Spikes and power spectral density (PSD, V^2/Hz) from ECoG recordings.
Sharing/Access information
For further information about the data uploaded, please contact Prof. Bernd Kuhn (bkuhn@oist.jp)
Code/Software
Analysis_Scripts.zip -- Scripts to analyze in vivo calcium imaging data. Run script on MATLAB 2018 or newer versions and add all subfolders and functions to path.MATLAB Toolbox required are listed below.
- Statistics and Machine Learning
- Signal Processing
- Curve Fitting
- Image Processing
- Bioinformatics
- The script "Analyse_Calcium_ASO_01" goes from raw extracted calcium traces found in defined data folder which was extracted from the modified version of EZcalcium Ver_0.0.1.
- Different code segments are arranged in the following manner :
- Arrange the data into a big data container
- Save the data container file into your designated destination
- Generate Ca Freq, amplitude, pairwise correlation using main function "Ca_trace_frequency_amplitude"
- Function "Ca_trace_frequency_amplitude" use a number of subfunctions for pairwise correlation
- shuffle_data_create_ci_neuron: will create a threshold value for each pair of neurons based on shuffled data
- cosine_similarity_matrix: will create a pairwise cosine similarity based on the data
- For the linear mixed model analysis we created an Excel sheet "Reformated data _freq" then we ran the following Matlab scripts
- importreformatted_data: to import the data from the Excel sheet ( you can choose one of the first 4 sheets in the Excel file)
- LMEmodel_givendata: use the data created from 3.1 to build the LME model and display statistics.
- icc_calculate: use the data created from 3.1 to infer interclass correlation.