Molecular Methods Homepage

Overview

Lab Schedule

Link to Protocols Here

       Protocols for 604.03 Exercises

        Additional Protocol Resources

        Supplemental Protocols

        Stockinger Lab Protocols

Module1 - Recombinant DNA

        Background

            day 1-ligation

            day 2-transformation

            day 3-minipreps

            day 4-restriction digests

        cDNA sequences

        Resources

Distributed Resources for Genetic Analysis

          day 5 - DNA sequence analysis

Module 2 - DNA Libraries

          General Background

          Specific Background for Exercise

               Primary Screen

               Library Titration

          Q-Pix Manuals for picking and gridding

                Library address

          Supplemental Protocol

Module 3 - Genetic Analysis

            Schedule

            Specific Background

                DNA extraction -CTAB

                96-Well DNA extraction (alternative protocol)

                PCR for Module 3

                Sequencing PCR products

                Sequence Submission Form

                MCIC Sequencing resources

            Data Analysis Links

                Clustal X download

                Alternative Clustal X download

                Taxonomy tools

                Phylip

                TreeView

            Questions for Module 3

                Questions

                Questions V. 2.0

                Supplemental data

                    CD31

                    PTO

                    LEOH176

Module 4 Gene Expression

                Background Links

                    RT-PCR: The basics (Ambion)           

                    Quantitative RT-PCR: pitfalls and potential (abstract)

                    Animation describing RT-PCR

                Background

                RNA extraction protocol

                Supplemental Protocols Quantifying RNA and RNase free glassware and reagents

Module 5 Protein purification     

                Background

                Protein extraction protocol

Supplemental protocols

Additional resources

1. Genetic Engineering and Biotechnology website at Colorado State University

http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/index.html

• Gel Electrophoresis of DNA
• Restriction Endonucleases  

2. Molecular Genetics course page at Oklahoma State University

http://opbs.okstate.edu/~melcher/MG/MGW4/MG428.html

• Molecular cloning
• bacterial transformation
• restriction mapping

3. Molecular Toolkit:

A group of programs for analysis and manipulation of nucleic acid and protein sequence data.

http://arbl.cvmbs.colostate.edu/molkit/index.html

Restriction enzyme mapping program (within Molecular Toolkit):

http://arbl.cvmbs.colostate.edu/molkit/mapper/index.html

4. Programs available on the web for restriction site analysis

Mapper

In silico Restriction

Web Map

Rebase

NEB cutter

Webcutter

EnzymeX

Restriction mapper 

WatCut 

5. Laboratory protocols guides

• Molecular Cloning A Laboratory Manual. Sambrook, Fritsch and Maniatis (often referred to as Maniatis). Cold Springs Harbor Press.
• Current Protocols in Molecular Biology. Wiley and Sons, Inc.
• Short Protocols in Molecular Biology (A compendium of methods from Current Protocols in Molecular Biology.
• Promega Protocols and Applications Guide