Contents 1 Protocols 1.1 In vivo 1.1.1 Escherichia coli 1.1.2 Comamonas testosteroni 1.2 In vitro 1.2.1 Nucleic acids 1.2.2 DNA 1.2.3 RNA 1.2.4 Protein 1.3 In silico 1.3.1 Data analysis 1.3.2 Databases 1.3.3 Modelling 1.3.4 Sequence analysis 1.3.5 Structure analysis 1.4 Miscellaneous 1.4.1 Cell culture 1.4.2 Microscopy 1.4.3 ILDs / Improvised Lab Devices

Protocols

The following page(s) gives an overview of the protocols and possible modifications that where used and proven working during the iGEM PET.erminators project 2012.

In vivo

Escherichia coli

• Bacterial cell culture
• Bacterial transformation aka TRAFO
• Cell counting/plating
• Chemically competent cells
• Colony PCR
• Electrocompetent cells
• Electroporation
• Engineering BioBrick vectors from BioBrick parts/Colony PCR
• In-fusion BioBrick assembly
• Miniprep / Qiagen kit
• Transformation of chemically competent cells
• Western Blot

Comamonas testosteroni

• Reviving a freez dried cell culture

In vitro

Nucleic acids

• Agarose gel electrophoresis
• PCR techniques
• SOE-PCR

DNA

• Agarose gel electrohporesis
• Annealing and primer extension
• Annealing primers
• Assembly PCR
• Cloning
• DNA Ligation
• DNA Quantification / NanoDrop
• DNA Synthesis from Oligos
• Engineering BioBrick vectors from BioBrick parts/Colony PCR
• Miniprep
• PCR
• Polyacrylamide gel electrophoresis
• Primer Design
• Purification of DNA
• Restriction digest
• Resuspension of primers
• Salting Out
• Sequencing DNA

RNA

Protein

In silico

Data analysis

• R Programming
• Mathlab / Simulink

Databases

• PDB
• CAS

Modelling

• SVEN!!!

Sequence analysis

• BLAST
• SAGE

Structure analysis

• PDB
• Protein structure prediction
• RNA secondary structure prediction

Miscellaneous

Cell culture

• Pouring LB plates

Microscopy

• Determining an objects size
• Preparing slides
• Staining

ILDs / Improvised Lab Devices

• x bp Primer Designer
• Enhancing a thermo cyclers cooling capabilites
• Gel pocket size reduction
• Growing iGEMlers