Dataset for manuscript titled: Female mice exhibit resistance to disease progression despite early pathology in a transgenic mouse model inoculated with alpha-synuclein fibrils

This repository contains the source data and code for the analyses in the manuscript titled "Female mice exhibit resistance to disease progression despite early pathology in a transgenic mouse model inoculated with alpha-synuclein fibrils", accepted for publication at Communications Biology.

Main subject file csv: masterfile-all-timepoint-data.csv

however additional csv files used for analysis are as following:

PT-WH-behavioural-data-bytrial-for-coxanalysis.csv -- data structured by trial to enable cox analysis

symptom-and-survival-tracking-data.csv -- symptom tracking and survival information provided separately

sex-difference-western-blot-data.xlsx -- western blot data collected and analyzed by Vladislav Novikov and Rodrigo Sandoval Contreras

All *.R files are R code scripts and named according to the analysis performed

Behavioural analyses

survival-plot.R           

symptom_profile.R

weight-rotarod-plots.R

PT-cox-analysis.R

PT-cox-analysis-sex-specific.R

WH-cox-analysis.R

WH-cox-analysis-sex-specific.R

Deformation-based analysis: voxel-wise volume trajectories

dbm-template.mnc

dbm-template-mask.mnc

DBM-models-and-peak-voxel-plots.R 

linear models:

M83-HuvsPBS-model.rds 

M83-HuvsPBS-model-females-only.rds  

M83-HuvsPBS-model-males-only.rds 

M83HuPFF-MvsF-model-male-effect-female-reference.rds

statistical maps for the 4 linear models:

DBM-statsmap-M83-HuvsPBS.mnc  

DBM-statsmap-M83HuvsPBS-withsex.mnc

DBM-statsmap-M83-HuvsPBS-females-only.mnc  

DBM-statsmap-M83-HuvsPBS-males-only.mnc

DBM-statsmap-M83HuPFF-MvsF-male-effect-female-reference.mnc   

Orthogonal projective non-negative martix factorization analysis  

4 OPNMF runs were performed: 1) 90 dpi all subjects; 2) 90 dpi female only; 3) 90 dpi male only; 4) 120 dpi all subjects

each run has an .R script, 6 minc files containing the spatial pattens for each of the 6 output components, and a csv file containing the subject weights