NOTE: The funding terminates July 30th 2007, and we are thus unable to accept new project applications.
Applying To Use Resource
Please take time to read the overview below about experiment design considerations and guidance for sending samples to us and using the resource.
Once you are happy to proceed please fill out a project proposal form below.
Experiment Design Considerations
Depending on the researchers requirements we can make the experiment as simple or complicated as needed. As experiment design is the most critical
part of planning any microarray experiment it is worth taking significant time to plan correctly. We strongly recommend any researcher to discuss this
with us carefully as it will effect the quality and significance of results obtained when using the resource.
One of the most fundamental considerations is the biological question that a researcher hopes to answer using the resource array. What interesting comparisons are
to be considered between different sets of samples (e.g strains, mutants, wildtypes, timepoints etc) will help establish a framework for designing the experiment and
enable the most efficient use of materials. Such considerations will be determined by the amount of RNA or DNA material avalible to carryout the experiment sufficiently.
We have the statistical tools to make direct comparisons between samples (those in the experiment design that are used for labelling) and tools for indirect comparisons
(those that are not included in the experiment design or labelling process but may be of interest). The advantage of indirect comparisons are the cost in materials is
significantly reduced compared to physically labelling every possible permutation. As this involves a statistical inference about the relationship between sample comparisons
and there is no physical comparison being made, this process will have it's limitations.
Therefore we advise that during the experimental design process the researcher is clear about
which comparisons are the most important to their research and uses these for any direct comparison. Indirect comparisons often highlight unforseen patterns and
relationships between samples and there is often the possiblilty of expanding experiments to make direct comparisons of any interesting data obtained from them.
Below are some examples of possible experiment design using mutant vs wildtype RNA populations and some basic timecourse possibilities using
classical and loop design approaches.
1) Basic design is a simple comparison between two samples.
2) Classical time course comparing several time points back to time zero.
3) Loop design is considered to give better and more robust results than the classical approach.
4) A more complex variation of the loop design with direct comparisons between several time points.
One advantage of a loop design is that indirect comparisons can also be made between time points that are otherwise unrelated (directly).
We highly recommend the use of loop designs as they are the most flexible approach to obtaining high quality data.
Guidance for using the Resource
We prefer that RNA/DNA preperation and extraction is done in the researcher's own lab using standard published procedures.
When sending samples to the resource we require the following sample details to carryout the experiment sufficiently.
1) Sample tubes clearly labelled with sample name.
2) Sample concentration clearly displayed on tubes and/or sample form.
(This should be carried out using spectrophotometer or other appropriate equipment).
3) Minimum of 25ug/sample of RNA, 5ug/sample of DNA.
(ideally double these amounts to allow for unseen circumstances during labelling and hybridisation).
4) Gel images from agarose gel or similar.
5) Samples preferably sent in ethanol at room temperature as we have found this the safest option for transporting samples.
(samples can also be sent on dry ice but due to variable courier service we can't guarantee results).
6) Number of biological replicates.
(We highly recommend using three biological replicates for each sample used in the experiment to allow for biological variation between samples).
(however we are flexible and this may depend on the number of experiment comparisons being made and wether the experiment is part of a pilot project or in depth
experiment.
7) Number of technical replicates.
(We generally do two technical replicates for each of the biological replicates one for the forward (Cy5/Cy3) and on for the reverse(Cy3/Cy5) dye orientations).
Project Proposal Form
Please inform us if you wish to carryout some or all of the experiment as you wish. We are happy for visiting collaborators to carryout
their own labelling and hybridisation in our laboratory and use our software tools if appropriate for analyses of their own data.
Please contact us if you wish to discuss any details of using the microarray resource.
The Small Print: By embarking on a project with the Dictyostelium Microarray Resource Group, you agree:
(a) to appropriately credit (e.g. by co-authorship) members of the group
for their input into the project.
(b) to make all microarray data available for submission to ArrayExpress or similar public database.