Comments: I finished the majority of the description sheet for SRP100604 and SRP268884. The only columns that need to be filled out are Category and Color. I need some input on the category column as I'm not too sure about the grouping. The Color column can be finished by Dr. Loraine or myself I just need confirmation on which. I will attach the spreadsheet file and move the task for review so we can finish the spreadsheet together and discuss everything at our next meeting if that is something you would like to do.
SRP100604_SRP268884_sample_sheet.xlsx
[~aloraine]

Since this was first worked on, I made some updates and changes to the format for the sample sheets. Please check with me on the details!

Per the previous comment, I have uploaded a new version of the spreadsheet, using the new format I mentioned.

In this new spreadsheet, please add / change the following:

1) Fill in the new column "publication" by adding the link to the PubMed record for the publication associated with the dataset. Review the SRA records. If the publication is not listed, google search. Usually searching for the "SRP" number will find the publication. Find the record in PubMed and add a link to it in this column.

2) Edit "treatment" column as follows:

• Change "cooler temperatures" to "cool"
• Change "elevated light conditions" to "high light"
• Change "nitrogen deficiency" to "low N"
• Change "warm temperatures" to "warm"
• Change "drought stressed" to "dry"

3) Double-check the genotypes. "JDE-13" looks like like it could be a replicate label, not a genotype. Genotype usually means something like a cultivar (e.g., "Moneymaker") or a transgenic line created by the investigator to test a hypothesis about gene function. For example, F3H-Ox3 is the name we've given to a transgenic line we created to see what happens when the enzyme designated as "F3H" is over-expressed. A genotype can also refer to a mutant line. For example "ARE" is a mutant in which the native F3H gene is disrupted, leading to an interesting phenotype which we are studying in the pollen project.

4) Change Tissue Type "five-leaf stage" to indicate what the sample actual is. Five-leaf stage of what? An entire seeding, the above-ground part, what is it? (You may need to look at the publication's methods section to determine what this is.)

5) In column "Category", use a single-letter code to indicate replicate samples. This is to ensure that downstream code can correctly perform statistical analysis, e.g., comparing groups.

6) I added two columns - "Study Name" and "Color". Leave these blank.

Here is the new Sample description sheet for SRP100604 and SRP268884:
SRP100604_SRP268884_sample_sheet.csv

Change requests:

• Please see the previous comment. Note that I made a new version of the Excel spreadsheet and replaced the one you made with this new version. The new, third version should be made by editing the second version.
• The second version I uploaded and attached was an Excel spreadsheet with a lot of formatting. Please use that to create the requested third version and save it in the exact same format, using the same xlsx file extension. The file added as a candidate third version is a "csv" file, not an excel spreadsheet, and so lacked the formatting.
• Publication column is in the wrong place in the third version. Observe that the publication column in the second version is already there but is empty. Please edit that existing column.

V3_SRP100604_SRP268884_sample_sheet.xlsx

Let me know if I formatted this new version 3 file correctly!

[~aloraine]

I can use this. Thanks