This page provides in-house protocols as well as manufacturer user guides for procedures and equipment used in the CMB.  The user guides are for various pieces of CMB equipment that are helpful to refer to for reminders of things said during formal training.  The protocols are to be used as a starting point from which you can modify based on your particular sample type or goals.  Please don’t hesitate to contact Riccardo Racicot for any help with deciding on modifications to make.


Sanger Sequencing

Sanger Sequencing protocol using BigDye Terminator v3

BigDye XTerminator – A more thorough way to clean up your seq rxns

96-well plate Sequencing purification using sephadex G50


Optimizing Sanger Sequencing for Longer Reads and in general

NGC – How Much DNA to Use for a Successful Sequencing Reaction

Direct colony sequencing

3500 video user guides and applications by ThermoFisher


Things you can do with your own DNA

DNA Extraction from Cheek Cells

Purification of total DNA from animal saliva using the DNeasy® Blood and Tissue Kit

Ethanol Ppt of DNA  Extra info on EtOH precipitation – DNA Precipitation-EtOH or Isopropanol

Mitochondrial Sequencing

DNA Fingerprinting protocol

RE determination of PTC tasting genotype

Chromosome prep and stain

Creating a Karyotype from your metaphase spread with Photoshop

Determine your orientation at your Xq28 locus


Gel Electrophoresis and Transilluminators

Gel Electrophoresis Protocol

User Guide for Transilluminators in the CMB



cDNA: Synthesis using Genisphere, labelling, and hybridization to a microarray – CMB

cDNA: Synthesis using Genisphere, labelling, and hybridization to a microarray – CWZ lab

How-to-Use Guide for GenePix 4100 Scanner and 4.1 Software (powerpoint)

GenePix Software-Tutorial



Quantitative Real Time PCR

TRIZOL RNA Isolation

How-to-use guide for the 7300

Analyzing your QRT for relative 2^-∆∆Ct

Notes for the StepOne Plus system and designing your QRT PCR Experiment

Interpreting melt curves

Considerations when adopting published sequences for your own qPCR assay

18_Real-time qPCR assay design guide_v8

Recommended dye combinations for multiplex qPCR


Digital PCR

Digital PCR Workshop

Digital PCR_Troubleshooting

Digital PCR Teaching Videos by ThermoFisher



How-to-use guide for the M5 plate reader and SpectraMax Software in the CMB

Quick Guide to the Plate Reader

How to export results files from the plate reader into Excel

How to Use Guide for the Nanodrop Spectrophotometer

4 tips for accurate oligo quantitation on the nanodrop

A Practical Guide to Analyzing Nucleic Acid Concentration and Purity with Microvolume Spectrophotometers



Guidelines for Using the Qubit 2

Protocol for Qubit DNA BR Assay

Protocol for Qubit DNA HS Assay

Protocol for Qubit RNA Assay

Protocol for Qubit Protein Assay

Protocol for Qubit ssDNA Assay

If you have a protocol you would like to share with others, or if there is a protocol you would like to see on this page, please contact the CMB’s ITI, Riccardo Racicot, at and let them know.  Thank you.