RNA-seq profiling of post-hypoxic head and neck cancer cell lines

Hypoxia is an important cause of radiotherapy resistance in head and neck squamous cell carcinoma (HNSCC). To investigate the transcriptional expression associated with post-hypoxic survival, we performed RNA-seq profiling of HPV-negative (FADU) and HPV-positive (SCC154) hypoxia-fate-mapped cell lines, hereafter called FADU-hfm and SCC154-hfm. Non-hypoxic (DsRed-positive) and post-hypoxic (GFP-positive) cells were sorted from 3D hfm-spheroids using fluorescence-activated cell sorting (FACS) and analyzed under normoxic conditions. The resulting dataset provides gene expression profiles of non-hypoxic and post-hypoxic cells.