RNA was extracted from plasma cells (PC) of wildtype (WT) mice and plasma cells (PC) from mice expressing a Myc short hairpin RNA (myc mutants). WT PC RNA is reverse transcribed in the presence of Cy3 dCTP (red) and myc mutant PC RNA is reverse-transcribed in the presence of Cy5 dCTP (green). Afterwards, both WT and myc mutant cDNA's are hydridized to a mouse microarray chip.

(1) At the end of this experiment, what color is the spot containing the Myc gene?
(2) What color spots correspond to genes that are NOT regulated by Myc?

(3) Many genes can be down-regulated by JQ1. What color would most of the spots corresponding to JQ1-down-regulated genes be in this experiment?

(4) If you wanted to verify that the myc mutant mice had changes in production of Myc protein, what experiment would you do? Describe briefly in 1- 2 sentences.

You have developed a small molecule compound (called iHOPE ) that you hope activates a histone deacetylase that acts specifically on the chromatin near the Myc gene. Design a microarray experiment to test your hypothesis. Make sure your answer includes " If, then " sentences that describe how you will draw your conclusions.