L-DOPA induces spatially discrete gene expression changes in the forebrain of mice with progressive loss of dopaminergic neurons

This zenodo project contains data from the project aimed at deciphering L-DOPA-induced changes in gene expression in the forebrain of dopamine-depleted mice (a model of Parkinson's disease), using spatial transcriptomics.

The dataset consists of the following files:

Phenotypic datasets

genotypes.csv - list of mouse used in the experiment and their most important characteristics
nor_boris_input.csv - data obtained from the Novel Object Recognition (NOR) test, used for analyses in R
nor-objects.xlsx - schedule for placement of objects in the NOR test
.mpg files - raw files recorded for each mouse during the NOR test
nor_preludium_2_cohorts.boris - file with the analysis of the NOR test in the BORIS software
rotarod_preludium.xlsx - results of the accelerating rotarod test
open-field.csv - results of open field test
oss-joint.csv - results of the operant sensation seeking test
.xlsx files with "RunStatistics" phrase in the filename - results from CatWalk XT sessions
files starting with "weight_" - weight measurements  for each mouse in the 2 cohorts, for each of two experiment periods recorded separately
.tif files with the phrase "gamma" in the filename - fluorescent microscope images of brain sections with green signal derived from the presence of TH

Transcriptomic data

.RData files - large R files with SeuratObjects, used for analysis
.tif files named after samples (e.g., "S5023Nr1.tif") - bright field microscope images of forebrain H&E-stained sections used in spatial transcriptomic analyses and visualization
.json files - derived from .tif H&E tissue images and created with Loupe Browser; used in spaceranger analyses
results.tsv - list of 121 differentially expressed genes across different clusters (181 records in total)
table_for_heatmap_reads.csv - table with data used for creating heatmaps
cluster_markers.csv - list of marker genes for each cluster, a result of FindAllMarker function in the Seurat software
.pdf files - depict spot assignment to clusters on a UMAP and corresponding to their spatial coordinates on the H&E sections images
files_and_samples.csv - a table connecting mice IDs, sample IDs and slide IDs