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| Status |
Public on Jun 05, 2017 |
| Title |
Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2 [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Over activation of NF-κB has close relationship with hepatitis and hepatocellular carcinoma (HCC). In this study, by manipulating NF-κB activity with its recognized activator TNFα and using ChIP-seq and RNA-seq techniques, we identified 699 NF-κB direct target genes (DTGs) in a widely used HCC cell line, HepG2, including 399 activated and 300 repressed genes. In these NF-κB DTGs, 216 genes (126 activated and 90 repressed genes) are among the current HCC gene signature. Functional annotation revealed that NF-κB DTGs in HepG2 cell are mainly related with many typical NF-κB-related biological processes, such as immune system process, response to stress, response to stimulus, defense response and signaling pathways of NF-kappa B. Some NF-κB DTGs are also involved in Hepatitis C and B pathways. The NF-κB DTGs were further confirmed by detecting the NF-κB binding and expression of 14 genes with ChIP-PCR and RT-PCR.
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| |
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| Overall design |
ChIP-seq of NF-kB in TNFα-induced and TNFα-uninduced HepG2 cells with two biological replicates.
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| |
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| Contributor(s) |
Dai W, Wu J, Zhang S, Shi B, Xu X, Wang D, Wang J |
| Citation(s) |
28579529 |
| BioProject |
PRJNA385785 |
| |
| Submission date |
May 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Dai |
| E-mail(s) |
[email protected]
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| Phone |
2583793620
|
| Organization name |
Southeast University
|
| Lab |
State Key Laboratory of Bioelectronics
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| Street address |
Sipailou 2#,Nanjing, Jiangsu Province, P. R. China
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210096 |
| Country |
China |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE98985 |
Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2 |
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