RNA sequencing was performed on a single biological sample for each patient-derived xenograft model in the Mayo Clinic Brain Tumor Patient-Derived Xenograft National Resource.
For RNAseq, mice with orthotopic tumors were processed, coronal tumor sections were stained by hematoxylin and eosin, tumor region was outlined by a neuropathologist, and sister unstained sections then were scraped to obtain tumor tissue.
RNA was extracted and then processed for RNAseq. The RNAseq was performed over several distinct time frames with slightly different technologies.
The RNAseq from all three time frames was processed through a common bioinformatics pipeline.