RNA-Seq Analysis of 70 MB Cancers

RNA-Seq was performed in this cohort of 70 MB cases as described in a previous study [8 (link)]. Briefly, RNA-Seq was run in a Nextseq 500 sequencing instrument (Illumina) for paired-end reads. The RNA-Seq data of this cohort are available in Gene Expression Omnibus (GSE143940 and GSE158413). RNA-Seq raw data were aligned by Kallisto [67 (link)] and the gene expression table was extracted by the tximport [68 (link)] package in R environment. For clustering, unsupervised clustering analysis was performed based on the 10,000 most differentially expressed genes using the consensus clustering default parameters by Rtsne and validated by 22 subgroup-specific signature gene expression levels [69 (link)]. RNA-Seq results were sent to Taylor’s laboratory at the Hospital for Sick Children, Toronto, to help with counterpart clustering.