This github repository contains protocols, example code, and other lab related documents for the Buckley Lab in the Soil and Crop Sciences section at Cornell Universtiy.

This repo is meant as a references for members and friends of the lab.

Below are descriptions of each of the directories contained in this repo. Within each of the directories is another README file with more detailed descriptions of the contents.

For those of you who wish to add protocols to this repo, please follow the following conventions in the heading of your protocol:

• Title
• Original author with date
• Contributing authors with modification dates
• Description
• Protocol/code/etc.
• Any citations needed

We will make an effort to keep this up to date but please note that some protocols may be older or unused and might need modification for new equipment, software, or methods. If you see any mistakes or want to add/modify any protocols, please push your changes and contact a lab admin. This repo is a work in progress so we welcome any new protocols as they are designed.

Protocols for measuring characteristics of soil.

Protocols for running DNA on a gel. This includes gel purification as well as PippinPrep.

Protocols, scripts, and methods related to DNA amplification with PCR.

Protocols for preparing DNA for sequencing. Most are protocols work with post-PCR DNA.

Protocols for using the Buckley lab GCMS. Also includes scripts for GCMS data processing.

Protocols for running DNA on a gel including gel excision, size selection and Blue Pippin protocols.

This directory contains information reguarding use of the Buckley Lab server.

Manuals and protocols for using some of the Buckley Lab equipment including:

• SpeedVac: Used for DNA concentration