Transcriptome profiling of human glioma and normal brain tissues by rRNA-deleted total RNAseq

Purpose: To compare the coding and non-coding transcriptomic changes in human gliomas compared with normal brain tissues. Methods: Biopsies were collected from 85 adult glioblastomas, 18 lower grade gliomas, and 15 normal brain tissues. Total RNA was isolated using the Qiagen RNeasy Mini kit or Trizol reagent according to the manufacturer's instruction. Stranded, rRNA-deleted libraries were prepared using the Illumina stranded Total RNA TruSEQ kit according to the manufacturer's instruction. Sequencing was performed on Illumina HiSeq 4000 instrument according to the manufacturer instructions. Reads were aligned to the human genome GRCh38 using HISAT2 (Version 2.1.0). Read counts for each gene were quantified using HTSeq-count (Version 0.10.0) and then normalized by DESeq2 (r package, version 1.20.0). Results: Approximately 20 million paired-end reads at the length of 50 bp were obtained from each sample. The genome mapping efficiency was 85% on average for all samples. Altered expression of 6,132 protein-coding genes and 1,270 lncRNAs were identified. Conclusions:We report the coding and non-coding transcriptomic changes in human gliomas compared with normal brain tissues. Overall design: 85 adult glioblastomas, 18 lower grade gliomas, and 15 normal brain tissues were characterised by rRNA-depleted total RNAseq.