Supplementary Data

Reference:

Tao Zhou#, Yanhong Wu#, Shuai Li#, Xinyao Qiu#, Erdong Liu#, Zhihua Xie#, Xuebing Shi, Yani Zhang, Guosheng Ma, Wenbo Guo, Xiang Wang, Kaiting Wang, Xiaomeng Yao, Ji Hu, Siyun Shen, Shuai Yang, Xiaoqing Jiang^*, Jing Fu^*, Hongyang Wang^*, Jin Gu^*, and Lei Chen^*. Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression.

Deposit gallbladder carcinoma atlas raw data: CNP0004660, HRA009841

Gallbladder carcinoma atlas data analysis scripts: https://github.com/JulieBaker1/GBC_analysis

Epithelial program identification scripts: https://github.com/JulieBaker1/AIEPI

scRNA-seq data
All Single Cells	Gene-cell count matrix	Cell annotation matrix	Sample info matrix
Lymphoid Cells	CD4.RDS	CD8.RDS	NK.RDS	B_cells.RDS	Plasma_cells.RDS
Myeloid Cells	DC.RDS	MonoMacro.RDS	Neutrophil.RDS	Mast.RDS
Stromal Cells	Endothelium.RDS	Fibroblast.RDS
Spatial transcriptome data
Visium Spatial	GBC_025_P	GBC_055_P
Whole exome sequencing data
WES	Mutations	CNVs

Paired validation data is here available for download.