This week I will once again be using the UCSC Genome Browser ( http://genome.ucsc.edu ), this time to gather data on how PIR expresses the pirin protein (Kent, Sugnet, Furey, et al., 2002). One of the traditional methods of gene expression analysis is through the use of DNA microarray assays, a process in which a sample of mRNA is essentially reversed engineered into DNA through a Reverse Transcriptase Polymerase Chain Reaction (RT-PCR). RT-PCR synthesizes DNA by taking the mRNA sample and utilizing an enzyme known as reverse-transcriptase as well as a polythymine primer (mRNA has a polyadenine tail) to create a single stranded complementary DNA molecule to the mRNA sample by deducing the proper nitrogenous bases for the DNA strand given the nitrogenous bases of the mRNA. This single stranded complementary DNA (cDNA) can then be dyed and placed into the microarray with any number of single stranded genes and DNA polymerase, thereby allowing the gene DNA to bind to the cDNA (Unbound cDN...
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