Striatal Cholinergic Transmission in an Inducible Transgenic Mouse Model of Paroxysmal Non-Kinesiogenic Dyskinesia

Description

BEHAVIOR: Prism GraphPad file with AIMs and dystonia scores for all animals included in the study and exposed to vehicle, caffeine or quinpirole. EPHYS: Excel files contain 2-min-binned firing rates values for each recorded cholinergic interneuron before and after application of quinpirole or caffeine. Excel file "WTvsPNKD ChI firing baseline" contains firing rates only at baseline of all interneurons from different experiments, used to perform a nested analysis. Prism GraphPad files show the statistical analyses performed on firing rate data. FIBER PHOTOMETRY: Raw in vivo fiber photometry recordings (alldata[...].csv) acquired with Neurophotometric FP3002 system version 0.5.6 and Bonsai software + video recordings (video.avi) of freely moving mice during photometry acquisition. KeyDown files contain the timestamp of caffeine/quinpirole/vehicle injections. Video.csv files align video frames to photometry data. The analysis folder contains all the Matlab scripts used to analyze the data as described in "steps to reproduce". MICRODIALYSIS: Prism GraphPad file with values of ACh concentrations obtained from HPLC analysis of microdialysate samples obtained from all the animals included in the study.

Steps to reproduce

Behavior Pipeline: 1) Use bonsai workflow "animal_tracking_post" to track animal movement. 2) The first column of the animal tracking .csv the standard motion pixel value -- basically, how many pixels changed from one frame to the next. 3) The next two columns are x and y coordinates for the centroid of the animal. You can convert these to distance using the next script. 4) "distance_speed_fromBonsaiTracking.m" calculate instantaneous velocity as first derivative of the distance traveled and speed as absolute value of the derivative (Unit is pixel/webcam frame rate). Peak Analysis Pipeline: 1) Use "Peak_freq_analysis" script to pre-process photometry ACh signals found in "alldata[..].csv" files in columns denominated RegionG (green ROI) (deinterleave, fit and extract df/f), find peaks and make 1min bin peak frequency graph. 2) script will write csv file of movsum that will be combined in a single file with all experiments, manually average bins of 1min [average (1:60*fs) fs=100Hz] and import in prism to plot average graph +SEM. 3) Use "peak_analysis" script after previous one to compute peak properties (interevent intervals, Inst.frequency, prominence and widths) in discrete time windows (baseline, 10, 30 min after drugs). it will write csv files that will be imported in prism to calculate cumulative freq distributions. Time-Frequency Analysis: 1) Use "Wavelet_Analysis" scrip for each experiment in each genotype to obtain time-frequency spectrum. 2) "AvgCWT" script will make a cell containing all mice for each genotype, make each matrix the same size by adding nan and then take the average across individuals= group average time-freq spectrum. 3) "Avg_over_time" script will divide timeline in baseline, 10 and 30 min post injection and compute average across time, plot freq vs average power. 4) "Avg_over_freq": pick freq band of most relevance and average across frequency over time= time domain of power in that band. 5) "Zscore" will normalize the signal to the baseline in each subject and then compute the population average.

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