Skinny Genes Quality Assurance

Datas and Files

Skinny Genes Edited Raw Data

Electronic Lab Notebook

Milestone 1

• Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines

Milestone 2

• Created presentation about the article
• We divided up the work into sections and each focused on our assigned task (each was designated a slide(s) and figure(s))
• Also, worked on annotated bibliography

Milestone 3

• deleted Gweight and Eweight since not conducive to our dataset
• changed "YORF" to "ID" and "Name" to "Standard Name"
• sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
• Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together

Milestone 4

• The QAs worked on organizing the layout and naming the standard names and IDs. (Group worked alongside Prof. Dalquist due to complications)
• In essence, we put in a list of genes into the name translator and found ost of the IDs and standard names, but we had blanks for a good amount of genes.
• We used multiple websites which included: "ORF List <-> Gene List", Synergizer, Bioconductor package
• We recently received all the names to move on with our work.
• We spoke with other groups to ensure that column headers were consistent with how other groups structured the data.
• Deleted duplicate data under alias names
• Filled in missing gaps for names

Problems

• Data set had duplicate data as well as alias for the duplicate data
• Many IDs/Standard names still were missing
• Manual input was needed to resolve (along with Prof. Dalquist)

Data was no fully complete and research and conversion was needed to move the database project along

Milestone 6

• made sure that all of the rows of data were imported into the database for the expression table
• made sure that both the ID (SGD systematic name) and Standard Names were included in each expression table and correct

User Page

template: cdomin12

Assignment Page	Individual Journal Entries	Class Journal
Week 1	cdomin12 Week 1	Class Journal Week 1
Week 2	cdomin12 Week 2	Class Journal Week 2
Week 3	RAD53 / YPL153C Week 3	Class Journal Week 3
Week 4	cdomin12 Week 4	Class Journal Week 4
Week 5	IMG/VR Week 5	Class Journal Week 5
Week 6	cdomin12 Week 6	Class Journal Week 6
Week 7	cdomin12 Week 7	Class Journal Week 7
Week 8	cdomin12 Week 8	Class Journal Week 8
Week 9	cdomin12 Week 9	Class Journal Week 9
Week 10	cdomin12 Week 10	Class Journal Week 10
Week 11	cdomin12 Week 11	Skinny Genes
Week 12/13	Skinny Genes Quality Assurance	Skinny Genes
Week 15	Skinny Genes Deliverables	Skinny Genes

Assignment	Individual Journal	Shared Journal
Week 1	jcowan4	Class Journal Week 1
Week 2	jcowan4 Journal Week 2	Class Journal Week 2
Week 3	FAS2 Week 3	Class Journal Week 3
Week 4	jcowan4 Journal Week 4	Class Journal Week 4
Week 5	iDog Week 5	Class Journal Week 5
Week 6	jcowan4 Journal Week 6	Class Journal Week 6
Week 7	jcowan4 Journal Week 7	Class Journal Week 7
Week 8	jcowan4 Journal Week 8	Class Journal Week 8
Week 9	jcowan4 Journal Week 9	Class Journal Week 9
Week 10	jcowan4 Journal Week 10	Class Journal Week 10
Week 11	jcowan4 Journal Week 11	Skinny Genes
Week 12/13	Skinny Genes Quality Assurance	Skinny Genes
Week 15	jcowan4 Journal Week 15	Class Journal Week 15

Misc. Links

• User:jcowan4

• Template:jcowan4

• Bio DB Home page

Acknowledgments

1. I worked with User:ymesfin, User:Jcowan4, User:msamdars, and User:dramir36 for this assignment.

2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Cdomin12 (talk) 14:00, 25 November 2019 (PST)

References

• Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13