was dissected for each group to increase the efficiency of the mRNA extraction and cDNA library preparation.
Before library preparation, RNA was assessed for quality using the TapeStation System using the manufacturer’s recommended protocols. We obtained a RIN between 6 and 7 after laser microdissection of glioma tissue. A RIN of 6 was determined to be suitable for cDNA library preparation. Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics by the University of Michigan Bioinformatics Core. Reads were aligned to the reference genome including both mRNAs and Ensemble lncRNAs using TopHat and Bowtie2 . Default parameter settings were used for alignment, with the exception of: “b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
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