Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data: IHC data

Immunohistochemistry staining of adjacent tissue sections from two pediatric ependymal tumors (7316-509 and 7316-490). Each tumor was stained for CA9 (a marker of mesenchymal regions), IBA1 (a microglial marker), and GPNMB (a DAM marker). Microglia surrounding CA9+ mesenchymal regions of the tumor acquired a DAM state, marked by the expression of GPNMB, while microglia in neuroepithelial regions of the tumor do not have detectable levels of GPNMB. These are the raw IHC images for Figure 7 of https://doi.org/10.1101/2023.02.06.527318.