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.
CMB and SCHEDULER Guide
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
Sanger_troubleshooting_guide_v1
Optimizing Sanger Sequencing for Longer Reads and in general
NGC – How Much DNA to Use for a Successful Sequencing Reaction
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
RE determination of PTC tasting genotype
Creating a Karyotype from your metaphase spread with Photoshop
Determine your orientation at your Xq28 locus
Gel Electrophoresis and Transilluminators
User Guide for Transilluminators in the CMB
Microarrays
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)
Quantitative Real Time PCR
Analyzing your QRT for relative 2^-∆∆Ct
Notes for the StepOne Plus system and designing your QRT PCR Experiment
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 Teaching Videos by ThermoFisher
Spectrophotometry
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
Fluorimetry
Guidelines for Using the Qubit 2
Protocol for Qubit DNA BR Assay
Protocol for Qubit DNA HS 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 rracicot@smith.edu and let them know. Thank you.