Transcriptome analysis of RNA from cancer cells exposed to chronic hypoxia versus normoxia. 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. Overall design: 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.

本数据集包含6株癌细胞系的转录组数据，这些细胞系分别在常氧（21%氧气）或低氧（1%氧气）条件下传代20次。本研究开展转录组分析，旨在探究1%氧气低氧条件下的长期传代培养对6株癌细胞系的基因表达与可变剪接的影响。所选用的癌细胞系包括2株胰腺癌细胞系（MIA PaCa-2、Capan-1）、1株肺癌细胞系（H226）、1株乳腺癌细胞系（MCF-7）、1株结肠癌细胞系（HT-29）以及1株卵巢癌细胞系（SKOV-3）。这些细胞系从12株癌细胞系的组合中筛选得到，依据其低氧8基因特征（hypoxia 8-gene signature）的表达水平，它们分别表现出最高与最低的低氧敏感性。实验整体设计如下：针对每一株细胞系，分别收集长期低氧培养条件下的4份RNA样本（2份生物学重复与2份技术重复），以及常氧培养条件下的3份RNA样本（1份技术重复与2份生物学重复）；随后按照制造商说明书，采用人类Clariom™ D芯片检测试剂盒（Affymetrix, Applied Biosystems™）对所有样本进行全转录组分析。芯片样本杂交采用Genechip® Hybridization Oven 640（Affymetrix）完成；随后使用GeneChip Fluidics Station 450（Affymetrix/Thermo Scientific inc）进行洗脱与染色，并通过GeneChip™ Scanner 3000 7G（Affymetrix/Thermo Scientific inc）完成芯片扫描。采用转录组分析控制台（Transcriptome Analysis Console, TAC）对CHP文件进行分析，并以常氧培养的细胞为对照，对长期低氧培养细胞开展差异基因表达分析。