Planning a Screen
There are many aspects to take into account when planning a screen with us and it's important to break-down a suitable timescale. Here are our main points to consider.
From the concept of a screen, to a list of hits can take several months to over a year. Sometimes, what appears to be a simple assay, working well in a few samples on your bench, will not translate easily into a whole genome screen involving 18000 clones in duplicate. Some screens have failed, before they even got started, but most progress uneventfully to a list of validated hits.
Remember to take an assay, using hand pipettes and some tubes, onto a semi-automated platform using robotics requires tinkering. To break times down into its individual parts here are some SRSF suggestions.
- In our experience, to get into the assay development plate stage of screen optimization, can take anywhere between one and ten months from conception. This is usually the most testing part of whole process.
- So why does this take so long? Most screen ideas appear as part of brain storming sessions, or a direct need to identify specific genes in a process, or from supervisors having "spare consumables budget" to do fishing experiments for a scientist close to the end of their contract or studies. RNAi screens are great vehicles for generating "extra data" to get that next grant, but require serious planning.
- The planning can quite often manifest itself in the assay development part of the screen. Most time is consumed by developing algorithms for segmentation or by improving the ability with which the controls will work or by just defining how the screen will be done.
- The assay development plates provide an excellent resource to develop the assay. Once the assay development plate has yielded satisfactory results, we suggest to screeners to do both phosphatome and kinome screens before starting with the genome-wide screen. This often gives an idea of the logistics and micro-time planning needed before commencing on the genome-wide screen, as this collection of RNAi plates comes as a set of five they are easy to manipulate without to much trouble.
The genome-wide screen usually takes between five and ten days to do, but can take a month or so, in planning, growing cells, building up plasmid stocks etc. Remember, on those days that you are doing screening, make sure every details is planned to the nth degree. You don't want any surprises on screening days, because you forgot something obvious. With data processing, if using 'R' and HTS2, usually takes a few weeks to generate all the Z-scores and a list of top hits.
There are training videos available on our web site, through the registered users area, so please make use of them. If you are using more complicated algorithms, i.e., from the ImageXpress suite, then data processing can take much longer. We suggest you develop ImageXpress algorithms, including the journals and canned applications during the assay development phase of this work.