FlyRNAi.org – Bigger and Better

fgr.hms.harvard.edu home page.

fgr.hms.harvard.edu home page.

FlyRNAi.org was initially a website that supported genome-wide RNAi screening in Drosophila cultured cells, beginning in 2003, but has evolved into a  functional genomics platform that has much to offer to researchers in communities focused on Drosophila and beyond.

Hu et al (2016) in Nucleic Acids Research provide a synopsis of what the updated FlyRNAi.org has to offer and I encourage all insect researchers with a interest in functional genomics and genetics to spend some time exploring the site and check out Hu et al.  for a tour and explanation

Table 2 in Hu et al. nicely lays out the various resources on the site by associating them with simplified questions reflecting the objectives of a potential user.

For example, if you are interested in questions like “in what cells, stages or tissues is a particular gene expressed” you can use the tool DGET and you will be able to see a clear graphic representation of available data and you can drill down into those data if desired.

Sample output using Find CRISPR. Green dots are individual gRNAs that can be viewed and assessed upon clicking through to the data

Sample output using Find CRISPR with the insulin receptor gene as the search target. Green dots are individual gRNAs that can be viewed and assessed upon clicking through to the data

You might be interested in all existing cell RNAi reagents that target your gene of interest and for this you can use the tool UP-TORR.  Also with UP-TORR you can see if there are any existing fly stocks that could be used for in vivo RNAi experiments.

If you wanted to measure steady state transcript levels in your gene of interest using qPCR you can go to FlyPrimerBank to find useful primers.

gRNA data associated with a single gRNA using Find CRISPR

gRNA data associated with a single gRNA using Find CRISPR

Want to do some CRISPR/Cas9-based editing?  You can use Find CRISPR to locate predefined gRNAs.  You can see some parameters reflecting an evaluation of the gRNAs based on what we understand about gRNA design.   If you design your own gRNA you can us the CRISPR efficiency tool to see how it meets ‘best practice’ standards.

Perhaps of broader appeal are the collection of protocols at the Drosophila Protocols Portal.  This web portal is being beta-tested at the moment and links out to various protocols on lab websites, videos or publications with relevant information on a protocol.  The protocols are organized in a rational way that enables users to quickly find protocols of possible interest.  While designed for Drosophila these protocols can either be useful to researchers working on other insect systems directly or can provide a framework from which to develop orthologous protocols for other species.

So, while many insect researchers working on insects other than Drosophila may tend to overlook resources like this because they appear to be (and are to a large extent) very specialized for a particular species, there is much to be gained in becoming familiar with this platform and using its contents to drive and guide resource development in your insect system of choice.

Stephanie Mohr, Ph.D. and Director of the DRSC/TRiP Functional Genomics Resources at Harvard Medical School, Boston, MA, USA

Note that senior author Stephanie Mohr is a Participant in the IGTRCN and a recent speaker at the IGTRCN-organized Symposium at the 2016 International Congress of Entomology.

HU, Y., COMJEAN, A., ROESEL, C., VINAYAGAM, A., FLOCKHART, I., ZIRIN, J., PERKINS, L., PERRIMON, N. & MOHR, S. E. 2016. FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update. Nucleic Acids Research. doi: 10.1093/nar/gkw977. 

 

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