Imacarae Week 7

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Assignment	Shared Entries	Individual Entries
Week 1	Class Journal Week 1	----
Week 2	Class Journal Week 2	Imacarae Week 2
Week 3	Class Journal Week 3	HSF1/YGL073W Week 3
Week 4	Class Journal Week 4	Imacarae Week 4
Week 5	Class Journal Week 5	CancerSEA Week 5
Week 6	Class Journal Week 6	Imacarae Week 6
Week 7	Class Journal Week 7	Imacarae Week 7
Week 8	Class Journal Week 8	Imacarae Week 8
Week 9	Class Journal Week 9	Imacarae Week 9
Week 10	Class Journal Week 10	Imacarae Week 10
Week 11	Sulfiknights	Imacarae Week 11
Week 12/13	Sulfiknights	Sulfiknights DA Week 12/13
----	Sulfiknights	Sulfiknights DA Week 14

Purpose

• To understand the background of what we will be working on for the next few weeks.
• To get started on the experimental design of this experiment.

Background, Method, and Results

1. Open Excel spreadsheet for dCIN5 data:
   • Opened the worksheet labeled "Master_Sheet_<dCIN5>".
   • In this worksheet, each row contains the data for one gene (one spot on the microarray).
   • The first column contains the "MasterIndex", which numbers all of the rows sequentially in the worksheet so that we can always use it to sort the genes into the order they were in when we started.
   • The second column (labeled "ID") contains the Systematic Name (gene identifier) from the Saccharomyces Genome Database.
   • The third column contains the Standard Name for each of the genes.
   • Each subsequent column contains the log2 ratio of the red/green fluorescence from each microarray hybridized in the experiment, for each strain starting with wild type and proceeding in alphabetical order by strain deletion.
   • Each of the column headings from the data begin with the experiment name ("wt" for wild type S. cerevisiae data, "dCIN5" for the Δcin5 data, etc.). "LogFC" stands for "Log2 Fold Change" which is the Log2 red/green ratio. The timepoints are designated as "t" followed by a number in minutes. Replicates are numbered as "-0", "-1", "-2", etc. after the timepoint.
   • The timepoints are t15, t30, t60 (cold shock at 13°C) and t90 and t120 (cold shock at 13°C followed by 30 or 60 minutes of recovery at 30°C).
2. Counting replicates
   • Strain: dCIN5
   • There are 4 replicates for each timepoint in this strain.
3. Saving File:
   • Saved original Excel file under original name: BIOL367_F19_microarray-data_dCIN5.
   • Saved as a new name: BIOL367_F19_microarray-data_dCIN5_IM

Data & Files

dCIN5 Master Sheet: File:BIOL367 F19 microarray-data dCIN5 IM.xlsx

Conclusion

This week introduced us to data analysis and the background to the different components of our data. With visualization of the data, we will be able to further complete data analysis and results in the future.

Acknowledgments

• I would like to acknowledge that the instructions for data analysis were copied and modified to fit this electronic notebook.
• To DeLisa Madere, Mihir Samdarshi, and Emma Young, my group mates. We met in class to do the assignment.
• Except with what is noted above, this individual journal entry was completed by me and not copied from another source.

Imacarae (talk) 22:08, 16 October 2019 (PDT)

References

• Assignment by LMU BioDB 2019. (2019). Week 7. Retrieved October 16, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Imacarae_Week_7.