20.109(S14):Data analysis (Day7)

Introduction

Topic 1: document some of the lecture info on NHEJ key players, leading to

Topic 2: more about C401 inhibitor, and

Topic 3: more about colony-forming assay and staining approach

Topic 4: but the most interesting/fun will be flow analysis: mean vs median choice; breaking down the Day 5 equation a bit more

Oh, and just a word about the MCS/GC/etc. issue for context

Protocols

Part 1: Stain irradiated cell colonies

Option to do it on M3D1 if they want to grow longer for bigger colonies?

All in main lab: rinse w/ 2mL pre-warmed PBS, add 2 mL Coomassie for 1 hr w/shaking, save it afterward, rinse w/PBS again, let dry a little bit, then count colonies right away. (Suggestions for counting approach and how to decide which ones pass the threshold.)

Part 2: Flow cytometry analysis

1. On one of the lab computers, double-click on the FACS server shortcut.
   • Alternatively, on your own computer access 18.159.2.11 directly. Ask your instructors for the username and password.
2. Go to the April 2014 folder, then to Agi Stachowiak. Copy over both the T/R and W/F image sets to your laptop: the filenames begin "analysis-images" and only the dates differ.
3. Copy over just your own day of statistics, unless you really want access to all of the raw data in your back pocket: the .csv filenames begin "analysis-statistics" and only the dates differ.

First look at instructor mock/single/etc. samples plus own plots.

Then move to stats. Save-as Excel sheet, keep just what they need.

Prepare separate sheet with columns/calculations of interest.

Finally, copy in the data.

Add all B/G ratios and NHEJ ratios group Excel worksheet somehow?

For next time

Methods, as promised.

Reagent list

write something here or not accessible to edit

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