|
| Status |
Public on Aug 14, 2018 |
| Title |
Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes up-regulated in abdominal preadipocytes and 90 genes up-regulated in GF cells. Assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200kb of the transcription start site (TSS). Interestingly, only 14 of the 90 GF-specific genes (15%) had GF-specific accessible chromatin sites within 200kb of the corresponding TSS, whereas 25 of them (28%) had abdominal-specific accessible chromatin sites.
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| |
|
| Overall design |
Preadipocytes cultured from A and GF adipose tissue obtained from premenopausal apple-shaped women were used to perform transcriptome analysis by RNA-seq and assess accessible chromatin regions by ATAC-seq.
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| |
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| Contributor(s) |
Smith SR, Osborne TF |
| Citation(s) |
30477572 |
| |
| Submission date |
Aug 13, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Adeline Divoux |
| E-mail(s) |
adeline.divoux@gmail.com
|
| Phone |
4073037100
|
| Organization name |
Adventhealth
|
| Department |
Translational Research Institute
|
| Street address |
301 E. Princeton St
|
| City |
orlando |
| State/province |
FL |
| ZIP/Postal code |
32804 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE118500 |
Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes |
|
| Relations |
| BioProject |
PRJNA485805 |
| SRA |
SRP157800 |
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