Hi friends :) It's been a minute since I've posted, so I'm gonna catch y'all up with four blog posts this week. Get ready haha.
I mentioned that I'm in my last year at Penn State in my Productivity and Mental Health blog post. I've started trying to tie off all my loose ends in the Perry Lab; as one of the senior grad students, this means that I'm passing on all my knowledge to those that will be here when I'm gone. Diego and I have been tag-teaming training the newest grad students in "how we do things", and we wanted to come up with a doc that could be used as a sort of Perry Lab handbook. Our main goal was to give the newbies and undergrads our baseline protocols and pipelines so that we could point them in the right direction without just handing them our codes or giving them the answers. It was also important to us that everyone in the lab could edit and add to this doc.
Our lab already frequently shares Google Docs and Slides, so we decided that our first generation of this handbook doc might be effective as a slideshow. Information could be easily organized and color-coded and hopefully easy to locate (I'm a big fan of all of those criteria). Maybe we'll convert this Google Slides set into a lab Wiki at some point; I've heard that those can be effective but have yet to play with them. In the meantime, these slides all have hyperlinks to relevant Slack posts, websites for packages, and/or articles. We also decided it'd be helpful to have a list of "Slide contributors" available on each slide, so people who use this doc know who to ask if they have further questions.
I'm sharing JPEG images of the slides below. Please click on them if you'd like to check out, comment on, or even use our slide set for yourself. Or click here. Either way, please let us know what you think of them, or share with us how your lab/working group shares established tips and tricks with each other. Disclaimers: We are in no way saying that our lab's way for doing things is the right way. We work with what we have available to us in our departments and at the university, as all labs everywhere do. This is merely a collection of things we've found to be effective for the Perry Lab over the years. Also, the slides are pretty jargon-y, so I invite any of you unfamiliar with the words below to fall into a Googling rabbit hole of genomics awesomeness.
As the acting lab manager and safety officer for the past several years, I'm responsible for getting everyone oriented with the kits and things we've utilized in our various projects. As such, our Wet Lab Considerations slide starts with a brief list of the various source materials we've worked with in our attempts to harness biomolecules (DNA and/or RNA mostly) from our species of interest. I've left my micropipetting and stoichiometry training off this slide since some of our more computational projects don't necessarily need detailed wet lab know-how, just more of an overview of what goes on in there.
Most of us have entered into the world of genomics with minimal to no bioinformatics or coding experience (like me). Thus Diego and I decided to keep a slide like Perry Lab Cluster Notes handy for those of us who aren't yet fluent with bash commands or dealing with the Penn State cluster systems. Christina Bergey set us up for success and installed basically any module we could ever need onto the cluster. This slide is basically our ode to Bergey and all of her computational niftiness. Gosh I am going to miss working with her every day...
We then broke down everything we do to the raw read data we get back from sequencing, whether it be ancient or modern DNA. Stephanie Marciniak did a lovely job with the aDNA slides, so we modeled the modern ones off of hers haha.
We've also started adding things you could do once you've cleaned up the raw data a bit, as shown in the last few slides below. The only slide I haven't shared with y'all is our brainstorming slide as the very end of our lab's doc. We throw any idea for a slide on this one, and then delegate/collaborate as needed to get the info on there. As an example, I think Maggie's gonna add a slide or two on how to make figures both visually stunning and scientifically effective, since she's pretty great at that. I'll be sure to keep the version of these slides I've shared with y'all updated as we add to it. I can't wait to see where this all goes! I hope my lab mates find it helpful, and you all as well. Cheers!