Difference between revisions of "Kwrigh35 Week 12"
From LMU BioDB 2017
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====Importance and significance of this work==== | ====Importance and significance of this work==== | ||
====Experimental design of the microarray data==== | ====Experimental design of the microarray data==== | ||
| − | * | + | *The cDNA microarrays contained targets for 5,952 genes |
**cDNA microarray chip comes from "DNA Chip Research, Kanagawa, Japan" | **cDNA microarray chip comes from "DNA Chip Research, Kanagawa, Japan" | ||
*20μL of cDNA was mixed with 40μL of DEPC-treated water and 60μL of 2× hybridization solution. This solution was heated to 90°C for three minutes. | *20μL of cDNA was mixed with 40μL of DEPC-treated water and 60μL of 2× hybridization solution. This solution was heated to 90°C for three minutes. | ||
| − | ** | + | **Hybridization solution comes from "CyScribe first strand cDNA labeling kit" |
*The solution was then placed onto the array and incubated overnight at 65°C to allow hybridization to occur. | *The solution was then placed onto the array and incubated overnight at 65°C to allow hybridization to occur. | ||
*The microarray was scanned with a Scanarray 4000 scanner | *The microarray was scanned with a Scanarray 4000 scanner | ||
*The spots were located on the chip by GenePix4000 software. | *The spots were located on the chip by GenePix4000 software. | ||
| + | *Corrections were made to account for the variations in quality of the spots and "cut off was done at an average background 118 value of +2SD." | ||
| + | *20% of the data was used to calculate the Lowess fit at each point of a log-intensity vs log-ratio plot. The resulting curve was used to adjust the control value for each measurement. | ||
| + | *Multiple DNA microarray trial were run, and at least 5 independent cultures were used. | ||
| + | *Genes with hypridization ratios > 2.0 and < 0.5 in at least 3 out of 5 experiments were considered up-regulated or down-regulate (respectively). | ||
| − | including treatments, number of replicates (biological and/or technical), dye swaps. | + | |
| − | + | including treatments, number of replicates (biological and/or technical), dye swaps. also, a Flow Chart | |
====Results==== | ====Results==== | ||
Revision as of 04:34, 21 November 2017
Contents
Electronic Notebook
New Terms
Make a list of at least 10 terms for which you did not know the definitions when you first read the article. Define each of the terms and provide a citation for each term.
- Trehalose
- A non-reducing dissacharide found in many organisms in each kingdom. It is often used in stress response and as a transport suger, among other uses.
- Lunn, J. E. (Apr 2016). Sucrose Metabolism [Abstract]. eLS. John Wiley & Sons Ltd, Chichester. Retrieved from http://www.els.net [doi: 10.1002/9780470015902.a0021259.pub2]
- DEPC-treated water
Article Outline
Importance and significance of this work
Experimental design of the microarray data
- The cDNA microarrays contained targets for 5,952 genes
- cDNA microarray chip comes from "DNA Chip Research, Kanagawa, Japan"
- 20μL of cDNA was mixed with 40μL of DEPC-treated water and 60μL of 2× hybridization solution. This solution was heated to 90°C for three minutes.
- Hybridization solution comes from "CyScribe first strand cDNA labeling kit"
- The solution was then placed onto the array and incubated overnight at 65°C to allow hybridization to occur.
- The microarray was scanned with a Scanarray 4000 scanner
- The spots were located on the chip by GenePix4000 software.
- Corrections were made to account for the variations in quality of the spots and "cut off was done at an average background 118 value of +2SD."
- 20% of the data was used to calculate the Lowess fit at each point of a log-intensity vs log-ratio plot. The resulting curve was used to adjust the control value for each measurement.
- Multiple DNA microarray trial were run, and at least 5 independent cultures were used.
- Genes with hypridization ratios > 2.0 and < 0.5 in at least 3 out of 5 experiments were considered up-regulated or down-regulate (respectively).
including treatments, number of replicates (biological and/or technical), dye swaps. also, a Flow Chart
Results
Results of this study in comparison to the results of previous studies
Acknowledgements
- I'd like to thank the team Data Analyst/my co-presenter Emma Tyrnauer for working with me on the assignment this week. We talked during class, over text, as well as during our meet-up on Monday afternoon.
- I'd also like to thank my other team partners Blair Hamilton and Zach Van Ysseldyke for continuing to work diligently on their portion of the project. We communicated during class and via text.
While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Kwrigh35 (talk) 20:19, 20 November 2017 (PST)
Referneces
- LMU BioDB 2017. (2017). Week 12. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
- Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf
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