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| Status |
Public on Oct 25, 2012 |
| Title |
Short-term time course of the effects of 1α,25-dihydroxyvitamin D3 treatment on open chromatin regions in THP-1 monocytic leukemia cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Open chromatin regions have been shown to associate with the location of transcriptiotal enhancers, i.e., the binding locations of DNA-binding transcription factors. To investigate the effects of short-term treatment by the nuclear hormone 1α,25-dihydroxyvitamin D3 (VD), a specific ligand of the transcription factor vitamin D receptor, on chromatin accessibility, FAIRE-seq was utilized on the chromatin samples from THP-1 monocytic leukemia cells that were treated with 100 nM 1α,25-dihydroxyvitamin D3 for 20, 40, 60, 80, 100 and 120 min, or with vehicle (0.1% (v/v) ethanol) for 20 and 100 min.
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| Overall design |
THP-1 monocytic leukemia cells were treated with 100 nM 1α,25-dihydroxyvitamin D3 for 20, 40, 60, 80, 100 and 120 min or with vehicle (0.1% (v/v) ethanol) for 20 and 100 min. Chromatin sample from one biological replicate for each time point was subjected to the FAIRE-seq protocol and subsequent data analysis using an Input chromatin sample as control.
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| Contributor(s) |
Heikkinen S, Pehkonen P, Seuter S, Carlberg C |
| Citation(s) |
23093607, 24185200 |
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| Submission date |
Aug 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sami Heikkinen |
| E-mail(s) |
sami.heikkinen@uef.fi
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| Organization name |
University of Eastern Finland
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| Department |
Institute of Biomedicine
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| Street address |
Yliopistonranta 1E
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA172741 |
| SRA |
SRP014820 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40075_RAW.tar |
8.2 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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