Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing

Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA -sequencing for Fresh Frozen (FF) samples and targeted gene expression immune profiles (NanoString) for Formalin-Fixed, Paraffin-Embedded (FFPE) samples to characterize the TIME of ependymoma samples. RNA was extracted from FFPE samples (ST n=2, PF-A n=4)