Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 4
Release date: Nov 2 2011
Last update date: Jan 18 2013
Access: Public
Diseases: Colitis, Ulcerative, Crohn Disease, Inflammatory Bowel Diseases
Dataset link Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition - TRANSFORMED GROUP

Experimental Protocol


Surgically resected specimens were used for isolation of human intestinal microvascular endothelial cells (HIMEC). HIMEC monolayers derived from intestinal mucosa of four different subjects – 2 controls, 1 ulcerative colitis, and 1 crohns were cultured in 75cm2 tissue culture flasks coated with fibronectin. Cells were left untreated (unstimulated/non-transformed) or exposed to the combination of IL-1b 100 U/ml, TNF-a 100 U/ml and TGF-b1, 5ng/ml (TGFTNFIL1) for six days. HIMEC medium was changed every 3 days. Total ribonucleic acid (RNA) was extracted using a commercially available kit (Qiagen®). RNA was reverse transcribed into cRNA which was then hybridized to the Illumina HumanRef-8 v2 Expression BeadChip. The raw gene expression datasets were processed to remove outliers, log2 transformed and quantile normalized using R lumi software. Those genes that satisfied the FDR p-value threshold of < 0.05 or raw p-value of <0.001 were identified as significant for the functional pathway and network analysis.

Repositories


GEO

GSE15934

ArrayExpress

E-GEOD-15934

BioProject

PRJNA123047

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Contact


Florian Rieder