Eyoung20 journal week 6 - Revision history

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← Older revision		Revision as of 01:51, 10 October 2019
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	"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."		"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
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		+	[[User:Eyoung20\|Eyoung20]] ([[User talk:Eyoung20\|talk]]) 18:51, 9 October 2019 (PDT)

	==References==		==References==

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 ==Acknowledgements==
 I would like to acknowledge my homework partner [[user:Knguye66]] for her help in understanding this assignment, and [[user:Kdahlquist]] for her instruction on the topic that provided valuable information and understanding.
 ==References==

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 ==Acknowledgements==
 ==References==
 *Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., & Darnell, J. (2000). Molecular cell biology 4th edition. National Center for Biotechnology Information, Bookshelf.

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 ==Acknowledgements==
 ==References==
-Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., & Darnell, J. (2000). Molecular cell biology 4th edition. National Center for Biotechnology Information, Bookshelf.
+*Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., & Darnell, J. (2000). Molecular cell biology 4th edition. National Center for Biotechnology Information, Bookshelf.
-Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
+*Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
-Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. (Available on Brightspace)
+*Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. (Available on Brightspace)
-DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 278: 680-686.
+*DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 278: 680-686.
-LMU BioDB 2019. (2019). Week 6. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_6
+*LMU BioDB 2019. (2019). Week 6. Retrieved October 9, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_6
-Chapter 4 of Campbell & Heyer (2003)
+*Chapter 4 of Campbell & Heyer (2003)
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 ==Acknowledgements==
 ==References==
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 ===(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.===
 [[file:Eyoung20translationovertimegraph.png]]
 ===(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.)===

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 ==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.===
 ===(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.)===
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← Older revision		Revision as of 01:11, 10 October 2019
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	===(Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?===		===(Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?===
		+	I would expect the spots of Yaplp targeted genes to be very red at later time points in the experiment. Yaplp is a transcription factor that aids in the resistance of environmental stress, so the longer experiment the continues, the more stress the cell is under and the more these genes should be expressed to attempt to compensate.
		+
	===(Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?===		===(Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?===

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 ===(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?===
-You would expect the spots representing the glucose repressed genes to be very red, because TUP1 which is responsible for the repression these glucose repressed genes has been removed.
+You would expect the spots representing the glucose repressed genes to be very red, because TUP1 which is responsible for the repression these glucose repressed genes has been removed. Do to the removal there is nothing to stop or slow the expression of these genes meaning they will continue to increase in expression.
 ===(Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?===