Breast cancer bulk and single-cell RNA-seq analysis scripts and processed datasets

This repository contains all processed datasets and R scripts used in the study "Construction of a Type 2 Diabetes–Related Gene Prognostic Index in Breast Cancer and Tumor Microenvironment Mechanism Analysis at the Single-Cell Level" (Journal: PeerJ). Included materials: 1. **TCGA-BRCA data (model construction)**: - `filtered_data.csv`: Filtered expression matrix for prognostic model construction - `clin_filtered.csv`: Corresponding clinical information - `surv_filtered.csv`: Subset used for survival analysis 2. **External validation datasets (GEO cohorts)**: - `GSE20685_series_matrix.txt.gz` - `GSE42568_series_matrix.txt.gz` - `GSE86166_series_matrix.txt.gz` - `GSE183947_fpkm.csv.gz` - `GSE103001_series_matrix.txt.gz` (if used) - `GSE78220_PatientFPKM.xlsx` (melanoma, PD-1 therapy cohort) 3. **Single-cell RNA-seq data**: - `combined_seurat_updated.rds`: Processed Seurat object including counts, metadata, and cluster annotations - `GSE243526.rar`: Original single-cell expression matrices and metadata 4. **Analysis scripts**: - `code.rar`: R scripts for preprocessing, differential expression analysis, prognostic model construction and validation, and single-cell analysis **Dataset summary**: | Dataset ID | Data Type | Tissue | Disease | Case | Control ||------------|-----------|-------|--------|------|---------|| TCGA-BRCA | Transcriptome | Breast | Breast cancer | 1091 | 112 || GSE20685 | Transcriptome | Breast | Breast cancer | 327 | 0 || GSE42568 | Transcriptome | Breast | Breast cancer | 104 | 17 || GSE86166 | Transcriptome | Breast | Breast cancer | 366 | 0 || GSE183947 | Transcriptome | Breast | Breast cancer | 30 | 30 || GSE103001 | Transcriptome | Breast | Breast cancer | 22 | 22 || GSE78220 | Transcriptome | Skin | Melanoma, PD-1 treated | 27 | 0 || GSE243526 | ScRNA-seq | Breast | Breast cancer | 8 | 4 |