Mouse_lung_superinfection_ST

This is the spatial transcriptomics data of lung tissue of mouse models with super-infection. 4 conditions of infection were included. (N_1, N_2: Naive; S_1, S_2: Staph infection on day 6; F_1, F_2: Influenza infection on day 0; FS_1, FS_2: both Influenza infection on day 0 and Staph infection on day 6). Please find the detailed information in github https://github.com/TianhaoLiu829/Superinfection_ST.git and related publications in communications biology. 

File "lung_combine_after_batch.rds" is the combined seurat object of 8 samples. The related information for each spot was saved in metadata slot. This seurat object should be loaded before running the code in github. 

File "ST_lung_superinfection_raw_count.zip" is the zip file with the gene by spot matrix with raw counts and x,y location files for each sample.

File "Images.zip" includes the histology images paired with ST data.

File "Seurat.zip" and "Commot.zip" are two packages used in this study.