Focuses on leukocyte isolation followed by optional washing and platelet removal.

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This issue is for discussing the preface of our protocols book.

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• Work on RNA protocol todo list:

RNA-TODO:

• RNA ICE
• Storage/Sample Conditions
• Add RNase Away
• RNase free consumables (water, tips, etc.)
• Kits
• Trizol
• cDNA libraries
• cDNA kits

Gives the full qPCR protocol including material, experiment preparation, wet chemistry, and LightCycler 96 setup.

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This chapter walks the user through various "best-practices" techniques for molecular biology lab work. The topics include contamination, centrifugation, pipetting, experiment preparation techniques (reading, calculating, and pre-cleaning), and experiment techniques (testing, timing, writing, and post-cleaning).

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An introduction to sample collection and how samples should be handled and stored in specific circumstances including samples for (DNA isolation, 16s RNA isolation, RNA isolation, and fibroblast isolation).

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• Create a list of protocols to make.

We need an internal version of this so we can add email/names and other sensitive stuff #1

Maybe we can have a login for the website.

Covers the basics of PCR and then goes straight into our GoTaq protocol. Touches on restriction enzymes and the thermocycler as well.

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Lists some of the kits and begins to talk about creating an RNAse free workspace.

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I've added the Sample Collection chapter. It is currently just a place holder, but I'm going to add information about collecting samples for DNA, RNA, and microbiome (maybe). @sdhutchins I'm also gonna add some place holder section for scRNAseq and cell culture (fibroblasts).

It might also be good to touch on the process that I had to go through to get the rhesus blood, and to have access to the animal core (e.g. IACUC training and informed consent form for each protocol that you are on).

A separate protocol for capillary electrophoresis was made to guide people through the process of using the QiAxcel. It also covers how our data is organized and how it can be synced to a USB drive.

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This protocol focuses on using the CiVi = CfVf concentration formula, and the concept of stock, psuedo-stock, and working solutions.

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I was thinking yesterday that we could do a repo for a bioinformatics "book" or tutorial where we discuss different software, workflows, best practices, etc. for incoming people into the lab.

That would allow us to keep this focused mostly on protocols while including best practices for molecular/cell culture techniques.

Thoughts?

Discusses PCR, primers, restriction enzymes, electrophoresis, analyzing gels, and DNA sequencing.

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Lists the kits that we use for DNA isolation, and follows with various protocols that we use for blood, and solid tissues.

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Covers primer design, ordering primers, stock solutions, and working solutions.

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• Check the spelling and grammar of the book.
• Make sure everything is formatting nicely (#3).
• Make sure the sentences flow well together.
• Make sure the chapters flow well.

Much of the Appendix hasn't been written yet, so this issue will stand as a placeholder. The current design of our appendix looks like this:

A - Troubleshooting
B - Scaling Tables
C - Equipment and Manuals
D - Kit Protocols
E - Experiment Templates
F - Safety Information
G - Projects
H - Vendors

Feel free to comment on any of these. Scaling Tables is a weird one, but I can see having a table for cell culture stuff, for my blood DNA isolation protocol, and a few more items. However, the tables should probably just go in the appropriate protocol they are matched to.

This chapter is dedicated to the Quartzy inventory system that we are currently using. It covers the Quartzy inventory and requests tabs including our implementation of the Freezer Box inventory system that Quartzy provides.

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• Add one file per chapter, appendix, etc.
  • Update chapters that can be updated
  • Create new Issues as needing
• Update README.
• Do not add sensitive documents.
• Add LICENSE.
• Add .github folder with ISSUE/PR templates
• Add custom vallenderlab CODE_OF_CONDUCT.

Note: Do not reformat until the end of writing to eliminate needless formatting/reformatting.
Note: Do not commit build until later.

This chapter describes the thought processes behind various "isolation" techniques for our lab including leukocyte isolation (from blood), DNA isolation, and RNA isolation.

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The book review will be monitored through this epic. The review issues associated with the chapters, protocols, and appendices can all be attached to this epic. The issues attached to the chapters have a title associated with the chapter number, but they may change in the future due to re-ordering, additions, or deletions of other chapters.

Discusses qPCR, RNA sequencing, single-cell RNA sequencing, and 16s rRNA Gene (DNA) sequencing.

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I'm currently using a nested list for the qPCR protocol with HTML. It doesn't render it properly. After the second nest it only uses lowercase Roman Numerals.

This chapter uses rmarkdown to knit together the files in the protocols/ folder that contain molecular-based protocols for our lab. The included protocols are dilutions, leukocyte isolation, dna isolation, rna isolation, pcr primers, pcr, capillary electrophoresis, and qpcr.

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https://bookdown.org/yihui/bookdown/markdown-syntax.html#math-expressions

• The chapters could be more generalized by removing the protocols and putting them in their own chapter per protocol or putting them in the Appendix.

• The chapters need to be renamed to include more general terms like:

chapter_3: 
  filename: "03-molecular-isolation.Rmd"
  text: "Molecular: Isolation"
chapter_4:
  filename: "04-molecular-pcr.Rmd"
  text: "Molecular: PCR"

• Move them to the appendix?
• Create a downloadable link?

I think that moving the protocols to the Appendix, and then providing a downloadable link would be a good thought.