Pt1200 e

The 27 RNA-seq datasets analyzed in this study were generated previously (5, 33 (link)). Frozen tumors underwent physical dissociation using a polytron PT1200 E homogenizer (Thomas Scientific) and total RNA was isolated using the Total RNA Purification Kit (Norgen Biotek) per manufacturer's instructions. RNA purity was quantified with the Nanodrop 2000 (Thermo Fisher Scientific) or Nanodrop One and RNA integrity was quantified with the Agilent 4200 Tapestation (Agilent Technologies). Libraries were prepared by the Cornell Transcriptional Regulation and Expression (TREx) Facility using the NEBNext Ultra II Directional RNA kit (New England Biolabs, E7760). Sequencing was performed at the Genomics Facility in the Biotechnology Research Center at Cornell University (Ithaca, NY) on the NextSeq500 (Illumina).

Frozen tumors underwent physical dissociation using a polytron PT1200 E homogenizer (Thomas Scientific), and total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek) as per the manufacturer’s instructions. RNA purity was quantified with the Nanodrop 2000 instrument (Thermo Fisher Scientific), and RNA integrity was quantified with the Agilent 4200 Tapestation (Aglient Technologies). Libraries were generated using the CleanTag Small RNA Library Prep Kit (TriLink Biotechnologies). Sequencing was performed on the HiSeq2000 or HiSeq3000 platforms (Illumina) at the Genome Sequencing Facility of the Greehey Children’s Cancer Research Institute (University of Texas Health Science Center). RNA from cell lines was purified and sequenced as described above except without polytron homogenization.