single-nucleus RNA sequencing (snRNA-seq) of matched samples of IDH-mutant low-grade glioma prior to and after treatment with safusidenib.
For snRNA-seq of fresh nuclei extraced from match pre- and post-treated tissue with safusidenib, 10,000 nuclei per sample were targeted on the Chromium controller, after which library preparation was conducted using the Chromium Next GEM single cell 5' v2 (dual index) kit (10x Genomics), following the manufacturer's instructions. For snRNA-seq of fixed nuclei (independent LGG cohort), nuclei were fixed for ~20 hours using the Chromium Next GEM single cell fixed RNA sample preparation kit (10x Genomics), according to the manufacturer's instructions. 10,000 nuclei per sample were targeted on the Chromium controller, after which library preparation was conducted using the human transcriptome Chromium Fixed RNA kit (4 reactions × 4 barcodes), according to the manufacturer's instructions (10x Genomics), with probe hybridisation conducted for ~19 hours. Libraries were sequenced on either a NextSeq 2000 or a NovaSeq X (Illumina), targeting 20,000 reads per nucleus.