Jnimmers Week 7
The data used in this exercise is publicly available at the NCBI GEO database in record GSE83656.
Methods
Begin by downloading the Excel file for your group's strain. Marcus & Jonar, Christina & Kaitlyn ( wild type data) Ivy & Emma, DeLisa & Mihir ( Δcin5 data) Iliana, Mike, Joey ( Δgln3 data) Aby, David, Naomi ( Δhap4 data) NOTE: before beginning any analysis, immediately change the filename (Save As...) so that it contains your initials to distinguish it from other students' work. In the Excel spreadsheet, there is a worksheet labeled "Master_Sheet_<STRAIN>", where <STRAIN> is replaced by the strain designation, wt, dCIN5, dGLN3, or dHAP4. 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 (steps 1-5 above having been performed for you already), 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). Begin by recording in your wiki, the strain that you will analyze, the filename, the number of replicates for each strain and each time point in your data.
Data and Files
File:BIOL367 F19 microarray-data dGLN3 JNM.xlsx
Biological Databases
Jnimmers
Assignment Table
