Protocols

This repo contains the various wetlab protocols and workflows used in the Pinsky lab

• Chemical Stock Solutions
• DNA Protocols
• RNA Protocols
• Nexterra Workflow
• PIRE Project
• Archived Workflows

Suggested Use

This is a complementary archived list of the protocols and workflows within the wetlab portion of the Pinsky lab. Our protocols are expected to change over time, it is best practice to take a snapshot of methods used at the time of your experiments. Doing so will create an archived version of the method that you can refer back to years later when you want to share a tip with someone or reference your work in a manuscript. Several workflows that are no longer in-use have been archived, though these protocols may contain useful procedures and insight into different methodologies.

Chemical Stock Solutions

DESS Stock Solution

EDTA Stock Solution

Lifton's Buffer

Low TE Stock Solution

NaCl Stock Solution

SSC/SDS Stock Solution

SSC Stock Solution

TE Stock Solution

TEN Stock Solution

Tris-HCl Stock Solution

Tris-Tween Stock Solution

DNA Protocols

Many of the protocols were created with the intention to be used for ddRADSeq. Reviewing the manufacturers' protocols is always highly recommended before beginning an experiment.

Baits Seq Capture

DNA Clean-Up

DNA Extraction

DNA Quantification

Digest

Ligate DNA

Qubit DNA

PCR

Pippin

Sequencing Prep

TapeStation 4200

RNA Protocols

The protocols listed below were originally intended to be used with the EecSeq Workflow. Please review manufacturers' protocols and workflows before starting a project.

Anneal Adapters

mRNA Capture

RNA Extraction

RNA Quantification

RNA Visualization

Nexterra Workflow

PIRE Project

https://sites.wp.odu.edu/PIRE/

Archived Workflows

EecSeq

This method was used in our Amphiprion percula clownfish project.

ddRADSeq

This was used in our Amphiprion clarkii clownfish project and our Paralichthys dentatus summer flounder project.

MRS Lab Notebook for Amphiprion clarkii