Transcriptome analysis of RNA from cancer cells exposed to chronic hypoxia versus normoxia

Transcriptome data from six cancer cell lines passaged twenty times in normoxia (21% oxygen) or hypoxia (1% oxygen) Transcriptome analysis was conducted to determine the effect of chronic, long passaging, at 1% oxygen (hypoxia) on gene expression and alternative splicing in six cancer cell lines. The cancer cell lines included were two pancreatic (MIA PaCa-2, Capan-1), one lung (H226), one breast (MCF-7), one colon (HT-29), and one ovarian (SKOV-3). They were selected from a panel of 12 cancer cell lines since they showed the highest and lowest sensitivity to hypoxia based on their expression levels of a hypoxia 8-gene signature. For each cell line, four RNA samples (two biological and two technical duplicates) collected from chronic hypoxia and three RNA samples (one technical and two biological duplicates) collected from normoxia were exposed to whole transcriptome analysis using the Human Clariom™ D Assay (Affymetrix, Applied Biosystems™) following manufacturer’s instructions. Sample hybridization to chip was done using the Genechip® Hybridization oven 640 (Affymetrix); washing and staining with the GeneChip Fluidics Station 450 (Affymetrix/Thermo Scientific inc) and scanning using the GeneChip™ Scanner 3000 7G (Affymetrix/Thermo Scientific inc). CHP files were analyzed using Transcriptome Analysis Console (TAC) and differential gene expression was conducted in cells exposed to chronic hypoxia compared to their normoxic controls.