1. Focus on the blue gene first. Look at the blue gene expression data in each of the four time points. Write down whether the gene is expressed a lot or not very much in each coverage plot (blue Tachyzoite stage, day3, day5, and day7).
2. Now focus on the red gene and describe its gene expression patterns in these four time points. Is there a lot or a little red gene expression for each time point (Tachyzoite stage, day3, day5 and day7)?
3. These next questions are related and ask you to compare what you observed in the above questions. What is the major difference between the way Toxoplasma gondii’s red and blue genes are expressed? At what time point do you see this difference? From what you know about these time points, are both these genes expressed in the same way when T. gondii is in humans and when it is in cats? Which gene is up-regulated—meaning there is a big increase in gene expression—in the cat compared to that in the human?
Advanced Question about Overlapping Gene Expression
Did you notice that there is blue gene expression (RNAseq data) that shows up not only under the blue gene, where you'd expect it to be, but also under where the red gene is? Conversely, there is a small amount of red gene expression that arises from the part of the genome where the blue gene is located (e.g., small blocks of red on the left side of the plot).
Why might this be?