Transcriptomic Analysis of Tumor Cells

Total RNA was purified from the tumor cells using the Direct-zol RNA Microprep Kit, according to the manufacturer’s instructions (Zymo Research, Irvine, CA, USA). RNA sequencing was performed by MedGenome Inc. (Foster City, CA, USA). Reference genome (mm10) and gene model annotation files from Ensembl were used for aligning reads using STARv2.5. The reads were quantified using HTSeqv0.6.1. A differential gene expression analysis was performed using DESeq2 v1.36. Ranked-log2 fold changes from the DESeq2 analysis were used as inputs for the analysis [61 (link)]. GO pathway enrichment was performed with clusterProfiler V4.0. A heatmap was generated using ComplexHeatmap v2.12.0. A ferroptosis pathway map was generated in Pathview v1.36 based on KEGG collections of the mouse ferroptosis pathway gene set. The entire dataset is deposited in GEO (accession # GSE213856).