Microarray experiments consist of various stages. Here, we aim to give a brief description of what these steps are along with detailed protocols. We also explain some of the pitfalls in performing them e.g. problems arising from the quality of the sample material, the labelling and hybridisation protocols and the data acquisition at the analysis stage.
The experimental stages can be broken down into four main areas;
1) Total RNA and DNA isolation
2) Qualitative and quantitative evaluation using the Agilent 2100 Bioanalyser
3) Hybridisations of DNA:DNA, RNA:RNA or RNA:DNA
Once these steps are carried out, analysis of the data can begin. The analysis steps are discussed within the Bioinformatics Section. Currently, there is no single standardised protocol for microarray experiments and the protocols described herein were specifically optimised for the study of C. jejuni, but could be modified for the study of other closely related prokaryotes.
Each experimental stage contains a short overview of the principles involved along with a detailed protocol.
Qualitative and quantitative evaluation with Agilent 2100 Bioanalyser