Measuring global gene expression

Development of DNA microarray technology (commonly known as microarray or DNA chip) has allowed simultaneous analysis of thousands of genes in a single sample

Monitoring and Evaluation of Biomaterials and their Performance in vivo.

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(Roth, 2002). Microarrays can be used to hybridize to RNA or DNA sequences; the former is used to measure the expression of multiple genes, while the latter is more commonly used to assess possible mutations in a genome (Goodkind and Edwards, 2005). It must be considered though: of the many thousands of genes contained within a genome, comparatively few of them are expressed within a cell at any given time.

Microarrays are substrates upon which oligonucleotide probes are printed and on which labeled transcriptome samples are applied. Before being applied on the microarray, the mRNA of interest is transcribed into stable complementary DNA (cDNA) and labeled with fluorescent, chemiluminescent, or radioactive tags. Subsequently, they are allowed to hybridize with the arrays where each cDNA can bind to the probes for each gene. Unbound cDNA is then discarded during the wash cycles following the hybridization, and based on the amount of hybridization that occurs, a signal is generated for each gene. There are many excellent review articles that focus on all the microarray technology available (Goodkind and Edwards, 2005; Groen et al., 2016; Hanagata, 2015; Roth, 2002).

Microarray-based gene expression profiling is often used to compare and contrast the influence of particular stimuli (e.g., growth factor, pathogen, biomaterial) on the mRNA abundance within a cell or cell population. While a powerful technique to assess thousands of mRNA transcripts simultaneously, the analysis of the generated data is complex, and the information generated can be difficult to interpret (Li and Wong, 2001). Furthermore, it is necessary to use PCR-based methods to confirm mRNA changes detected by microarrays.

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