In a RNA-seq study of tumor tissue from glioblastoma primary tumor tissue, a gro

Question

In a RNA-seq study of tumor tissue from glioblastoma primary tumor tissue, a group of up and down-regulated genes were identified (that is, the transcript levels were changed relative to control, normal tissue). Some of these genes represented known cancer genes, others were novel genes. Describe three (3) analyses you would conduct for only ONE of the up-regulated OR down-regulated (not both) novel genes. (That is, how would you determine the possible role of this gene in glioblastoma oncogenesis (if any). Remember, you would have the gene cDNA cloned and available vectors, glioblastoma cell lines, etc.) Include the following:

            1. The three different assays to analyze your gene of interest. OUTLINE the steps for each assay. That is, how will the experiment be conducted? What type of cells will you use? What will be measured? What will be graphed? What are the controls?

            2. The expected results for each of the assays.

Explanation / Answer

cDNA microarray analysis has been the best to find out the gene expression in cancerous cells compared to non-cancerous healthy cells. 2-dimensional gels have been helpful in separating different proteins based on their charge, mass and it paves way for gene expression. RNA extraction and RT-PCR analysis has been important before cDNA microarray analysis. Selection of differentially expressed genes in different cells of a tissue affected with cancer has been important. The characteraization and confirmation of these genes through 2-Dimensional gel has been very important.

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