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Series GSE67250 Query DataSets for GSE67250
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
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)
GSM1642984 NL3_MIGS
GSM1642985 NL4_MIGS
GSM1642986 NL2_MIGS
BioProject PRJNA279340
SRA SRP056520

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE67250_RAW.tar 945.2 Mb (http)(custom) TAR (of TXT)
GSE67250_RnaSeqCounts.txt.gz 583.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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