This directory contains all the files for the sgRNA sensor project. Below is a brief description of each directory:

data/

Miscellaneous data files, organized by type (e.g. gels, sequencing, flow cytometry, etc.)

analysis/

Python code for generating the sequences associated with all the various design names I use (e.g. rxb/11/1 => GUUUCA...)

documents/

Group meetings, presentations, manuscripts, etc.

flow_cytometry/ (git repository)

Scripts for analyzing flow cytometry data.

literature/

An out-of-date set of papers relevant to this project. I now keep my papers in a Zotero database that's not accessible from the file server.

orders/

Quotes for various things I've ordered. Not really useful for anything.

protocols/

Protocols relevant to this project, including the in vitro cleavage assay, electocompetent cell preps, and library screening. Does not include protocols that are generally useful for every project I work on.

scripts/

Generally useful scripts, for tasks such as designing cloning primers, quantifying the efficiency of electrocompetent transformations, and tracking the progress library screens.

sequences/

Snapgene files for all the plasmids that are being used in this project.

structures/

Pymol sessions for the Cas9/sgRNA complex, which are sometimes useful to look at.

notebook/

Plans and results for specific experiments, such as cloning and screening libraries.