|
| Status |
Public on Jul 17, 2014 |
| Title |
Diet-induced chromatin remodeling in mice livers |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
The tissue-specific packaging of the genome into the nucleus through chromatin is fundamentally involved in gene regulation, and aberrant modifications to chromatin are a hallmark of many diseases. We show here that a high fat (HF) diet leads to substantial chromatin remodeling in the livers of C57BL/6J mice, as compared to mice fed a control diet. Regions of the genome that display the greatest variation in chromatin accessibility between HF and control regions are targeted by transcription factors with known roles in the liver including HNF4α, CEBP/α, and FOXA1. Whereas livers of DBA/2J mice fed a HF or control diet also demonstrate diet-induced chromatin remodeling, the regions displaying the greatest variation are largely distinct from those observed in B6 livers, indicating a crosstalk between genetic and epigenetic components in determining how diet-induced chromatin remodeling is associated with metabolic disease progression.
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| |
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| Overall design |
Examination of chromatin remodeling with FAIRE-seq in livers of mice (C57BL/6J and DBA/2J) fed a high fat or control diet. Complemented with gene expression and H3K4me1 analyses
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| |
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| Contributor(s) |
Leung A, Parks B, Du J, Trac C, Setten R, Brown K, Lusis AJ, Natarajan R, Schones DE |
| Citation(s) |
25006255 |
| |
| Submission date |
Mar 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Leung |
| Organization name |
Beckman Research Institute, City of Hope
|
| Department |
Diabetes/Cancer
|
| Lab |
Schones
|
| Street address |
1500 E. Duarte Rd
|
| City |
Duarte |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (20)
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|
| Relations |
| BioProject |
PRJNA240124 |
| SRA |
SRP039411 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE55581_C57BL6J-Con-peaks.narrowPeak.gz |
505.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE55581_C57BL6J-HF-peaks.narrowPeak.gz |
500.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE55581_C57BL6J-all-peaks.bed.gz |
306.4 Kb |
(ftp)(http) |
BED |
| GSE55581_C57BL6J_gene_exp.diff.gz |
987.2 Kb |
(ftp)(http) |
DIFF |
| GSE55581_DBA2J-Con-peaks.narrowPeak.gz |
479.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE55581_DBA2J-HF-peaks.narrowPeak.gz |
432.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE55581_DBA2J-all-peaks.bed.gz |
282.5 Kb |
(ftp)(http) |
BED |
| GSE55581_DBA2J_gene_exp.diff.gz |
974.7 Kb |
(ftp)(http) |
DIFF |
| GSE55581_RAW.tar |
2.3 Gb |
(http)(custom) |
TAR (of BEDPE) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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