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Electronic Lab Notebook

Purpose

The purpose of this assignment is to learn about DNA microarrays. It also is a way to learn about data and how we can organize data to derive meaningful information from experimental results.

Assignment Questions

(Question 5, p. 110)

Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.

ADD IMAGE HERE OF GRAPH

(Question 6b, p. 110)

Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)

X: Black, Dim Red, Black, Medium Green Y: Black, Medium Red, Dim Green, Bright Green Z: Black, Dim Red, Dim Red, Dim Red

(Question 7, p. 110)

Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?

Yes, X and Y, my explanation is this below: The genes all have ratios of 1.0 an hour in so they are not showing induction or repression yet. Then an hour in they have all been inducting but at different rates. Then 5 hours in they all split in what they are doing, Gene X is having no change in transcription, while Gene Y is starting to repress very slightly and gene Z is inducting again. Then at 9 hours, Gene X and Y are repressing a lot. All in all Gene X and Y are the most similar in terms of their transcription ratios here.

(Question 9, p. 118)

Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?

Most would be yellow in the first time point because there is no difference in levels of expression at the start. They show up yellow because one gene is using the green fluorescence and one is using the red, so they look yellow on the computer screen when they are imposed on one another. If two genes were expressed equally that would be the reason for an experiment to result in most spots being yellow.

(Question 10, p. 118)

(Question 11, p. 120)

(Question 12, p. 120)

(Question 13, p. 121)

(Question 14, p. 121)

(Question 16, p. 121)