The slidedeck can be found here (in Dropbox): IGB > Outreach > Conferences > 2024-ASPB > 2024-05-29-ContentSlides.pptx

For this first round of review, please take a look at this slidedeck alongside the workshop outline that's being finalized in IGBF-3744.

• Make sure that all key points from the outline are being covered by the slidedeck.
• Confirm that all of the images have been updated since the 2017 version of this workshop.
• Have a student run through the slidedeck on their own to make sure that the slides are easy to understand and follow.

After running through the workshop I made some comments on the powerpoint slides. In general I had made some formatting suggestions to make it easier for users to follow if they are using it after the workshop in case they forget some things that may be demoed.

On slide 43 specifically you had told users to select A.28.75.7, A.28.75.8, A.34.75.7, and A.34.75.8. In the IGB screenshots you had actually used the 45 minute replicates and the output you had provided was different because of that. Pretty easy fix!

Thank you for the comments, Dylan Marrotte! I've incorporated most of Dylan's suggestions from the comments that he sent to me via email and I've fixed the issue with the screenshots outlined above.

Ann Loraine and Nowlan Freese, please take a look at these slides before the workshop next week and let me know if you'd like to see any changes made. I've made some changes based on comments from both of you during the run-through that we did this morning.

Notes:

• The slides are great overall!
• Problem: I don't know where the term "transmutant" came from. That term is not really a term a plant biologist would recognize. Definitely do NOT use that term! The correct term or description for the VF36-T3 genotype is: "VF36 transformed with a construct consisting of the F3H cDNA driven by the 35S promoter." The best short-hand term to refer to this line would be "transgenic line" or "F3H transgenic line." Using the term "mutant" is super confusing because the genotype that got transformed was VF36, not a mutant of any kind, and the transgene itself encodes the wild-type allele of F3H.
• Slides 14 and 15 do a GREAT job of explaining what all the samples are. I think maybe you should try to show those during the presentation, after you explain all the navigation stuff in IGB (zooming, panning, jump-zooming, etc.) That way, I can skip the details of the experimental sample names and only do a high-level explanation of the experiment at the end of the Introduction.
• Slide 26 - suggest changing to: "RNA-Seq to genome alignments - "read" alignments for short"
• Slide 32 - add another slide before this recommending they zoom out to show the entire gene region and the entirely of all the RNA-Seq alignments. Then have them load the genomic sequence by clicking the "Load Sequence" button.
• I think you should explain (in the slides) about the RNA-Seq alignments piling up on top of each other in the top row of the RNA-Seq read alignment tracks.
• Edit suggestion for slide 48: (changing complex language to simpler language for better readability) "Now the Y Axis Scale is consistent across tracks!" to "Now the Y Axis is the same in selected tracks"
• Edit suggestion for slide 49: Change: "Several genes were identified by the statistical analyses as being differentially expressed in the are genotype after exposure to heat stress." to "Statistical analysis identified genes that responded differently to heat stress in are versus VF36 samples." This is because the figure (the heatmap) is actually making a bigger claim about the "are" genotype - it is claiming that the genes shown in the figure respond differently to heat stress depending on plant genotype. Note that to demonstrate this result in IGB, you have to include control samples and stress samples. So, if there is enough vertical distance available given the size of the laptop screen, I would recommend loading all three coverage graphs each of: (1) are control, 75 min (2) are treatment, 75 min, (3) VF36 control, 75 min and (4) VF36 treatment, 75 min.

Notes from Nowlan:

• Get rid of notes throughout the presentation
• Delete slide 5
• Delete top box on slide 6
• Remove the "1." From slide 6
• Get rid of slide 7
• Switch slides 13 and 12
• Fix numbers on slide 16
• Remove bullet point from slide 21
• Remove errant periods throughout presentation
• Remove numbers from slide 22
• Update images for slides 21-23 so that they're consistent with the other images being used
• Don’t cover the coordinates in slide 32
• Delete section headings

I've incorporated the changes suggested by Nowlan and Ann in the comments above this one. I will now work on publishing these slides to our Canvas course ahead of the workshop. Moving this ticket to Done.