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

ABSTRACT:

Background

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 samples and targeted gene expression immune profiles (NanoString) for formalin-fixed, paraffin-embedded (FFPE) samples to characterize the TIME of ependymoma samples.

Results

Our results showed a stable expression of the 40 housekeeping genes throughout all samples. The Pearson correlation of the endogenous genes was high. To define the TIME, we first checked the expression of the PTPRC gene, known as CD45, and found it was above the detection limit in all samples by both techniques. T cells were identified consistently using the two types of data. In additi

SUBMITTER: de Koning W 

PROVIDER: S-EPMC10361846 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature