This repository contains the code and scripts used for the single-cell/spatial transcriptomic analysis of mouse oligodendrocytes in Alzheimers disease. The data used in this project can be accessed using the following link :
- MARS-seq 2.0 data generated from whole WT and 5XAD mice brain : GSE202297
- Chromium 10X data from the hippocampi of TauP301L, PS2APP/TauP301L, and PS2APP/TauP301L/TREM2KO mice (Lee et al. 2021) : GSE153895.
- Smart-seq2 data from healthy and EAE mice (Falcão et al. 2018) : GSE113973
- Chromium 10X data from healthy and EAE mice at various stages of the disease (Wheeler et al. 2020) : GSE129609.
- Chromium 10X data from Aging SVZ (Dulken et al. 2019) : PRJNA450425
- Visium® 10X data from LPS injected mouse brains (Lee et al. 2021) : GSE165098.
Additionnaly, two small files are needed for the analysis :
- DOL_genes.txt : a txt file containing the list of the DOL genes
- tissue_positions_list.csv : a csv file with the correspondanc between Visium spot location and nucleotide barcode. It is needed for the analysis of the two Visium® datasets.
All those dataset were analysed using the pagoda pipeline. To install it please go on the corresponding Github page. Other packages need to be installed :
- fifer
- uwot, RColorBrewer, pheatmap, VennDiagram and liger (CRAN packages)
- DESeq2, GEOquery, biomaRt, ggplot2 and CountClust (Bioconductor packages)
This repository contains the following scripts :
- Whole_brain_analysis.R : script and thus containing all the code to generate Figure 1 (analysis of all non immune cells from the brain)
- EAE_Falcao_analysis_script.R : script for the analysis of the Smart-Seq2 EAE dataset.
- EAE_Wheeler_analysis_script.R : script for the analysis of the 10X EAE dataset.
- Aging_SVZ_analysis_script.R : script for the analysis of the 10X aging SVZ analysis.
- Visium_brain_inflamation.R : script for the analysis of the LPS stimulated brain samples.
- AD_hippocampi_analysis_script.R : script for the analysis of the hippocampi from various AD models.