This webpage was produced as an assignment for Genetics 677, an undergraduate course at the University of Wisconsin - Madison.
DNA Microarrays and Gene Expression
DNA microarrays can be used to measure changes in expression levels, to detect single nucelotide polymorphisms (SNPs), and to genotype or resequence mutant genomes.
Below is a Youtube video, DNA Test Methods - DNA Microarrays (1), explaining how microarrays work and their various applications.
Below is a Youtube video, DNA Test Methods - DNA Microarrays (1), explaining how microarrays work and their various applications.
GEO
Gene Expression Omnibus (2) is a search database for microarray data, searchable by gene name, organism, disease, etc.
Cystic fibrosis patients with mild and severe lung disease: GDS2143
Analysis of the nasal respiratory epithelium of cystic fibrosis (CF) patients with mild or severe lung disease. CF patients have identical homozygous deltaF508 CFTR genotypes but exhibit variability in pulmonary disease severity. Results provide insight into the basis of the phenotypic difference.
Analysis of the nasal respiratory epithelium of cystic fibrosis (CF) patients with mild or severe lung disease. CF patients have identical homozygous deltaF508 CFTR genotypes but exhibit variability in pulmonary disease severity. Results provide insight into the basis of the phenotypic difference.
DNA Microarray organized by UPGMA Hierarchal Clustering Algorithm
Mediator of RNA Polymerase II Transcription Factor 31 (MED31)
CF and small intestine: GDS588
Analysis of small intestine from 40 day old CFTR-/- and CFTR+/+ mice. The CFTR null mouse has a severe intestinal phenotype serving as model for cystic fibrosis related growth deficiency, meconium ileus, and distal intestinal obstructive syndrome.
Analysis of small intestine from 40 day old CFTR-/- and CFTR+/+ mice. The CFTR null mouse has a severe intestinal phenotype serving as model for cystic fibrosis related growth deficiency, meconium ileus, and distal intestinal obstructive syndrome.
Catalase (Cat)
Mast Cell Protease 1 (Mcpt1)
Analysis
These two microarray data sets were obtained from experiments testing CFTR null and control mice for expression levels of catalse and mast cell protease in the small intestine.
In each experiment, total RNA was prepared from the entire small intestine of three 40 day old CFTR control male mice, CFTR(+/+), and three 40 day old CFTR null male mouse, CFTR(-/-), using TRIzol reagent. Mice were fed Peptamen (100% enzymatically hydrolyzed whey) from age 10 days to prevent intestinal obstruction.
Catalase levels are found to be higher in control mice than the CFTR null mice. Mast cell protease 1 is found to be higher in CFTR null mice than controls. These expression levels are highly significant and more research is to be done in order to find how their levels affect or are affected by CF. They could be potential drug targets for the treatment of CF.
In each experiment, total RNA was prepared from the entire small intestine of three 40 day old CFTR control male mice, CFTR(+/+), and three 40 day old CFTR null male mouse, CFTR(-/-), using TRIzol reagent. Mice were fed Peptamen (100% enzymatically hydrolyzed whey) from age 10 days to prevent intestinal obstruction.
Catalase levels are found to be higher in control mice than the CFTR null mice. Mast cell protease 1 is found to be higher in CFTR null mice than controls. These expression levels are highly significant and more research is to be done in order to find how their levels affect or are affected by CF. They could be potential drug targets for the treatment of CF.
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References
1. DNA Test Methods - DNA Microarrays. Posted by PHG Foundation. March 21, 2010. (Youtube Video) http://www.youtube.com/watch?v=3jX_08zdYCE&NR=1
2. Gene Expression Omnibus (GEO). March 24, 2010. http://www.ncbi.nlm.nih.gov/sites/entrez
References
1. DNA Test Methods - DNA Microarrays. Posted by PHG Foundation. March 21, 2010. (Youtube Video) http://www.youtube.com/watch?v=3jX_08zdYCE&NR=1
2. Gene Expression Omnibus (GEO). March 24, 2010. http://www.ncbi.nlm.nih.gov/sites/entrez
Alexandra Reynolds
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