Extended Data Fig. 1: Overview of experiment design and comparison of bulk RNA-seq and scRNA-seq transcriptomic profiles from Ctrl and endometriosis tissues.

a, Experimental workflow. b, UMAP showing distribution of cell based on tissue types, PID, and endometriosis stage, before and after batch correction with Harmony. c, Box plot showing Spearman’s correlation rank (ρ) between bulkRNA-seq and pseudobulk from scRNA-seq in Eutopic (Ctrl & EuE, n = 144), Peritoneal (EcP & EcPA, n = 90), or Ovary (EcO, n = 24). Each dot represents a sample pair. The box represents the interquartile range with median and minimum/maximum represented by box centerline and whiskers, respectively. d, Scatterplot showing distribution of average gene expression between bulk RNA-seq and scRNA-seq (Spearman ρ). Each dot represents a gene. e, Volcano plots representing DEGs between scRNA-seq pseudo bulk (red) and bulk RNA-seq from undissociated tissue (blue) (edgeR, FDR < 0.001, LogFC > 3). The genes highlighted are exclusively expressed in bulk RNA-seq and associated with erythrocytes (orange), neuronal projections (green), adipocytes (brown), and muscle cells (purple). Related to Fig. 1.