|
| Status |
Public on Mar 22, 2016 |
| Title |
Integration of genome-wide DNA methylome and transcriptome of human intestinal fibroblasts reveals novel candidate gene signatures in Crohn’s disease-associated fibrosis |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Tissue fibrosis is a serious complication of Crohn’s disease (CD) as well as of a variety of other complex, chronic pathologies. Understanding the underlying pathophysiology of tissue fibrosis is crucial for the development of tissue-specific prevention and interventional treatment strategies. To identify molecular states specific to fibrotic disease, we employed deep sequencing to define the genome-wide DNA methylome and the whole transcriptome of purified human intestinal fibrotic fibroblasts (HIFs) isolated from the colon of patients with fibrotic CD. Integration of this information, via computational tools, identified candidate molecular interactions that could lead to fibrosis pathology. Our definition of a genome-wide fibrosis-specific DNA methylome provides a new paradigm for understanding mechanisms of pathological gene expression that lead to intestinal fibrosis and may have relevance to fibrogenesis in other organs.
|
| |
|
| Overall design |
Human intestinal fibroblasts (HIFs) were extracted and cultured from colon specimens of two groups: Crohn’s disease with associated fibrosis (n=3) and normal fibroblasts from patients with Diverticulitis (n=3). Both RNA-seq and MBD-isolated genome sequencing (MiGS) were performed on every sample.
|
| |
|
| Contributor(s) |
Sadler T, Bhasin JM, Xu Y, Barnholz-Sloan J, Chen Y, Ting AH, Stylianou E |
| Citation(s) |
26973718 |
| Submission date |
Mar 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Angela H Ting |
| E-mail(s) |
ahting@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Ting
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
Tx |
| ZIP/Postal code |
77054-1901 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA279340 |
| SRA |
SRP056520 |
Less...
More...