Additional file 2 of Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing

Additional file 2: Fig. S1. Sample collection, single-cell clustering and marker gene visualization for major lineages. Fig. S2. Immunohistochemistry (IHC) staining of immune cells. Fig. S3. Cluster marker genes, tumor cell identification, cellular fractions and hematoxylin eosin (H&E) staining for epithelial cells. Fig. S4. Upregulated genes and signatures for malignant cells among TN, MPR and NMPR patients and serum estradiol dynamics. Fig. S5. Marker genes, differentially expressed genes and RNA velocity for T/NK subsets. Fig. S6. Marker genes, immunofluorescence, and Nichenet analysis for B-cell subsets. Fig. S7. Marker genes and survival analysis for myeloid subsets. Fig. S8. Monocle, SCENIC and cellular fraction analysis for neutrophil subsets.