Buckley lab protocols

Introduction

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.

Adding protocols

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.

Printing

If you would like to print or download one of these protocols you can convert any document here into a PDF by replacing github.com/... in the URL bar to gitprint.com/... and either printing or saving the resulting PDF.

For instance, to print this README you would change https://github.com/buckleylab/Buckley_lab_protocols/blob/master/README.md to https://gitprint.com/buckleylab/Buckley_lab_protocols/blob/master/README.md. You may have to alter the print settings to make sure that the entire document fits in a standard page.

Or you can use the [Github Markdown Printer][(https://chrome.google.com/webstore/detail/github-markdown-printer/fehpdlpmcegfpbkgcnaleindodeegapk) Chrome extension.

Directories

DNA extraction

Protocols for extracting DNA and RNA from soil.

Gel electrophoresis

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

PCR

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

Preparing DNA for sequencing

Protocols for preparing DNA (post-PCR) for sequencing.

Amplicon library processing

Scripts for processing raw sequence reads from Illumina MiSeq.

Robot

Spreadsheets and directions for using the robot.

HR-SIP

Protocols for conducting an HR-SIP experiment.

GCMS

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

Soil chemistry

Protocols for measuring chemical and physical characteristics of soil.

PLFA

Protocols for conducting phospholipid fatty acid extraction.

Working in lab

Guidelines for conducting oneself in lab.

Using the server

Guidelines and directions for using the Buckley Lab server.

Lab equipment

Manuals and protocols for using some of the Buckley Lab equipment.