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| Status |
Public on Aug 01, 2015 |
| Title |
Subsets of NFkappaB-dependent genes are differentially regulated after combined treatment with hyperthermia and cytokine |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Heat shock transcription factor 1 (HSF1) is responsible for triggering stress-induced activation of the HSP genes. HSF1 is also involved in the regulation of many other genes associated with multiple cellular processes including cell signaling, development, fertility, cell death and metabolism, e.g. NFkappaB transcription factor. Here we aimed to establish a global picture for the association between hyperthermia-modulated expression of NFkappaB-dependent genes and HSF1 binding in regulatory regions of target genes. The global pattern of HSF1 binding was analyzed after 10 and 20 minutes of hyperthermia using the ChIP-Seq approach. The analysis revealed about 25,000 HSF1 binding sites in chromatin of control untreated U-2 OS cells, which nearly doubled in cells subjected to hyperthermia. The presence of hyperthermia-induced HSF1 binding was established in regulatory regions of hyperthermia-affected genes and in TNF-affected genes. In most cases hyperthermia pre-conditioning inhibited cytokine-mediated activation of NF-κB-dependent genes. However, our results also revealed novel gene subsets that included TNFalpha-regulated and hyperthermia-unaffected genes, as well as genes (co)repressed, (co)stimulated, or antagonized by both types of stimuli.
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| Overall design |
On Illumina platform we sequenced DNA immunoprecipitated from U-2 OS cells using anti-HSF1 antibody. Cells were either untreated (control) or heat shocked for 10 and 20 minutes. Two PCR-verified ChIP replicates were collected per each sample.
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| Contributor(s) |
Janus P, Tomasz S, Piotr W |
| Citation(s) |
25944781 |
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| Submission date |
Sep 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tomasz Stokowy |
| E-mail(s) |
tomasz.stokowy@uib.no
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| Organization name |
University of Bergen
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| Department |
IT Division
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| Lab |
Scientific Computing
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| Street address |
Nygardsgaten 5
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| City |
Bergen |
| ZIP/Postal code |
5020 |
| Country |
Norway |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA260042 |
| SRA |
SRP045982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60984_RAW.tar |
3.3 Mb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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