Electronic notebook: sinorhizobium meliloti

Week 12

• Read the paper on the salinity and sucrose stress on gene expression
• Sorted the raw data into an XML file
• started to compile the raw data
  • downloaded all raw data and sorted through the information needed
  • used the cys5 and cys3 fold change as well as all the IDs
• Uploaded 300 NaCl compiled data set

Week 13

• I continued to sort the raw data and began to process the data in an xls file
• this was a very repetitive part because it involved a lot of replications for each time set
• finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
• Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
• preformed a Tstat test
• Preformed a Pvalue test
• added a row of N next to the gene ID name in the forGenMAPP tab
• uploaded Processed Data
  • NOTE:the GenMAPP version of the tab is labeled Complete Processed data_MPM and not forGenMAPP

week 15

• I worked on some of the mistakes that I had made in my prior data sets
  • removed AVG_LOGFC_ALL row
  • added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
• sanity check concluded the number of genes significantly changed at each time point
  • T15- 5520
  • T30- 7484
  • T60- 6711
  • T240- 5901
• Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
• uploaded XLS Version and TXT version, USE THIS

• had to change names of the columns in order to correctly upload to GenMAPP
  • system code column was renamed
  • Gene ID column was renamed to ID on the Programmers computer to resolve some issues
• it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP
• ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded.

Reflection on the Process

What did you learn?

• With your head?
• I learned a lot about gene expression and metabolic pathways and how the cell responds in many ways to a single stimulus. Also I learned a lot about the principles of coding and how to organize a query in language that the computer understands
• With you Heart
• I learned that people need to keep in contact every few days and need the latest updates on your progression in the work. Also coordinating with your team in order to tackle a broader objective that contains many parts and disciplines, it was really rewarding to see that we all started working on the project at completely different ends but came together in the end with a single final result.
• with your Hands? (technical skills)

I learned to organize and operate GenMAPP and map finder with enough proficiency that I could probably do it again if I was given the same project but on a different species. I also learned how to format things in a way that the computer could read and understand what I wanted in order to get a desired result What lesson will you take away from this project that you will still use a year from now?

• The lessons that I will take away from this project was that you need to understand the gist of where your partners are in their work even if you don't understand what they are doing. This will allow you to get a general idea in mind about when your job and their job will meet and could give you insight if there is a discrepancy between your work and their. In other words a problem that arises when your part of the project meets theirs but cant be found out until both of the pieces of work come together