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| Status |
Public on Dec 20, 2008 |
| Title |
Hypoxic shock in DLD-1 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Combining our full-length cDNA method and the massively-parallel sequencing technology, we developed a simple method to collect precise positional information of transcriptional start sites (TSSs) together with digital information of the gene expression levels in a high throughput manner. We applied this method to observe gene expression changes in a colon cancer cell line cultured in normoxic and hypoxic conditions. We generated more than 100 million 36-base TSS-tag sequences and revealed comprehensive features of hypoxia responsive alterations in the transcriptional landscape of the human genome. The features include presence of inducible hot regions in 54 genomic regions, 220 novel hypoxia inducible promoters that may drive non-protein-coding transcripts, 191 hypoxia responsive alternative promoters and detailed views of 120 novel as well as known hypoxia responsive genes. We further analyzed hypoxic response of different cells using additional 60 million TSS-tags and found that the degree of the gene expression changes were different among cell lines, possibly reflecting cellular robustness against hypoxia. The novel dynamic figure of the human gene transcriptome will deepen our understanding of the transcriptional program of the human genome as well as bringing new insights into the biology of cancer cells in hypoxia.
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| Overall design |
Gene expression changes were observed in DLD-1 cells in response to hypoxic shock (1% O2).
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| Contributor(s) |
Suzuki Y |
| Citation(s) |
19237398 |
| |
| Submission date |
Dec 19, 2008 |
| Last update date |
Feb 22, 2018 |
| Contact name |
Yutaka Suzuki |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
University of Tokyo
|
| Street address |
4-6-1, Shirokanedai
|
| City |
Minatoku |
| State/province |
Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
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| Platforms (1) |
| GPL4133 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) |
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| Samples (1) |
| GSM352624 |
DLD-1 cells in response to hypoxic shock (1% O2) |
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| Relations |
| BioProject |
PRJNA112409 |
