How we normally work on collaborative microarray projects
We do not provide a 'service' in which we simply process RNA / microarray samples and provide people with data. This is because: we are not set up or funded to do so; we have no particularly interest in doing so; and because this approach fosters bad microarray experiments. We will occasionally process a small number of slides with / for a new project if this is for a proof-of-concept purpose, or to generate preliminary data for a subsequent project, but as a rule we expect and train people to do their own microarray experiments.
Overall, the pattern for no two microarray projects is the same and some or all of the following steps contribute to different projects.
We can simply supply people who are already experienced with these methods with microarrays. In this setting we normally will discuss the purpose of the project, and specifically the experimental design and number and nature of planned experimental replicates. Sometimes we will be involved again at the data analysis stage, and other times not.
Sometimes a group will come to us with a new project for which no existing microarray exists, or for which the microarray platform has not been selected. In this setting, we will go through the whole of the objectives of the project, and define whether an existing or bespoke array is the most appropriate, and proceed from there.
If a new microarray is needed, then we will consider the best type of tool, for example oligo- or PCR product-based, and work with the group for primer / probe design, the generation of the products, and then we will print the arrays with the layout and replication best suited to the experiment.
Sometimes, most frequently, a group will want to use one of our existing microarrays. We will then sit down, talk through the experiment and it's design, ensure that a microarray is the best / a suitable tool for the experimental objective, and usually it will be decided that we will either go through a process of training during the first replicates of the experiment until the relevant people are consistently generating good data. At this point, if the group is set up to perform these studies themselves they may continue their work in their own laboratories, or, if not, they will complete their studies with less supervision / input with us.
Depending upon the availability of BlueFuse, once a group has been trained to use this tool with us (if they are not already familiar with it) then they will either do their analysis with us, or back in their own laboratories. This part of the microarray process can (should!) be quite time-consuming if done properly, particularly if working with microarrays with large number of probes that are poorly (not) replicated. This can be a point of 'congestion' with our current resources, and groups with a significant number of arrays are encouraged to establish this resource for themselves, especially if they are not based locally.
The use of BASE facilitates collaborations with groups outside of the Department, and outside of Oxford, because it is a web-based system that allows people to perform, upload, and download their work from remote sites. It also enables us to curate and look at datasets that people are working on remotely, and to assist with questions related to analysis. At this point we often also help with assessing the quality and nature of the data collected, and in the decisions upon whether additional replicates or experimental comparisons are needed, or whether more focussed replication using Q-RT-PCR is more appropriate, or needed in addition.
Finally, at the stage of publication, we have a number of array definition files, and protocol information, which we maintain with the EBI to facilitate efficient submission of the data to ArrayExpress.