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New! RNAseq/Transcriptomics/Next-Gen Sequencing Service Offered by the FR3 Molecular Division
The FR3 Molecular Division is pleased to announce the availability of a new RNAseq/transcriptome service for the filarial research community. The FR3 Molecular Division can assist in all phases of a project including experimental design, preparation of RNA from parasites, library preparation, Next-Gen sequencing on the Illumina platform, and bioinformatics/data interpretation.
Pilot projects have been successfully completed with the laboratories of Tom Unnasch and Tim Geary. Descriptions of these projects can be found below. Projects will be done on a cost-sharing basis with the FR3 and so the total cost of the projects are quite low (contact Jessica Grant for details at firstname.lastname@example.org).
If you are interested in submitting a proposal for a collaborative RNAseq project with the FR3, please submit a brief proposal that includes specific aims, a research strategy and an NIH biosketch to email@example.com and firstname.lastname@example.org. In your proposal, be sure to address the following:
Significance –What important problem does the study address? How will scientific knowledge be advanced? What is the potential impact of these studies to the field?
Approach–the conceptual framework, design methods, and analyses should be adequately developed, well integrated, and appropriate to the project. The project should be technically feasible. Demonstrate knowledge of the capabilities and limitations associated with RNAseq experimental design.
Proposals will be reviewed by the FR3 Directors (Steven Williams, Andrew Moorhead and Michelle Michalski) with a second level of review conducted by the Scientific Advisory Committee to the FR3 (SAC). The SAC current membership includes Patrick Lammie, Timothy Geary and Lyric Bartholomay.
Statement on the FR3 RNAseq Project from Tom Unnasch (University of South Florida):
“Steven Williams and the FR3 team at Smith helped my graduate student complete a project to define the physiological role that the ecdysone response pathway plays in Brugia malayi. We cultured a number of biological replicates in the presence and absence of ecdysone and did a transcriptome analysis to identify the transcripts up-regulated in the worms treated with ecdysone. My bioinformatics collaborator, when looking at the data commented that these were the tightest biological replicates that she had even seen. We were able to identify a number of transcripts that were up-regulated in the worms treated with ecdysone. We chose four that appeared to demonstrate different levels of up-regulation for confirmation by RT-PCR. The ddCt values for the four genes matched the results that we got from the RPKM analysis almost exactly. All in all, the sequencing project gave a technically very satisfying result that we are currently writing up for publication with members of the FR3 team”.
Statement on the FR3 RNAseq Project from Tim Geary (McGill University):
“Steven Williams and the FR3 team at Smith helped a team of graduate students from McGill and Georgia complete a comprehensive project on transcriptomic analyses of drug responses in Brugia malayi maintained in culture. We were delighted to have the students work at Smith to assist with sample preparation and learn the basics of RNAseq analysis. Our analyses involved multiple biological replicates with variables that included drug, drug concentration and time of exposure. Our data analyses confirm the very high quality of the replicates, which provide exceptional value for teasing out drug effects on this parasite. Unquestionably, the sequencing project gave us important and technically very satisfying results that we are currently writing up for publication with members of the FR3 team”.