SignedPPI included in list of "Signaling Breakthroughs of the Year"

How cool is this? SignedPPI, which was developed by the Perrimon lab and DRSC, made it onto the Signaling Breakthroughs of the Year list at Science Signaling!

Here's the paper that describes SignedPPI (free in PubMed Central): Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, Samsonova AA, Neumüller RA, Mohr SE, Perrimon N. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods. 2014 Jan;11(1):94-9. PMID: 24240319; PMCID: PMC3877743.

Large-scale in vivo RNAi screen for factors related to germline stem cells

Yan D, Neumüller RA, Buckner M, Ayers K, Li H, Hu Y, Yang-Zhou D, Pan L, Wang X, Kelley C, Vinayagam A, Binari R, Randklev S, Perkins LA, Xie T, Cooley L, Perrimon N. A regulatory network of Drosophila germline stem cell self-renewal. Dev Cell. 2014 Feb 24;28(4):459-73. PMID: 24576427.

From the abstract: "... To comprehensively identify components of these networks, we performed a large-scale RNAi screen in Drosophila female germline stem cells (GSCs) covering ∼25% of the genome. The screen identified 366 genes that affect GSC maintenance, differentiation, or other processes involved in oogenesis. Comparison of GSC regulators with neural stem cell self-renewal factors identifies common and cell-type-specific self-renewal genes. ..."

These authors deposited screen data into RSVP, the TRiP's RNAi Stock Validation and Phenotypes data repository. Additional data submissions welcome!  Check it out online here.

CRISPR knock-in approaches in Drosophila.

Scott J. Gratz, Fiona P. Ukken, C. Dustin Rubinstein, Gene Thiede, Laura K. Donohue, Alexander M. Cummings, and Kate M. O'Connor-Giles. Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila. Genetics genetics.113.160713; early online January 29, 2014

DRSC announces launch of FlyPrimerBank online resource

The DRSC is pleased to announce the launch of FlyPrimerBank.

FlyPrimerBank is built around a database of three precomputed qPCR primer pairs per Drosophila gene. Online search output includes information about the primer pairs and when available, validation test results from our group or the community at large.

For details please see our paper, just out in the journal G3. You can also check out the documentation page.

Important for RNAi studies, FlyPrimerBank can report overlap between the primers and RNAi reagents in public collections. This helps you avoid choosing primers that could amplify the reagent.

As always, your feedback on the online resource is welcome.

FlyPrimerBank also makes it possible for you to indicate which qPCR primers in FlyPrimerBank have or have not worked for them, or to upload the sequences of good primer pairs not already in the database.

With your help, the utility of the resource will further increase over time.

UP-TORR. A new tool from the DRSC. Find RNAi reagents--using today's information!

The DRSC has launched a new tool! 

And a corresponding paper is now out in the journal Genetics.

Hu Y, Roesel C, Flockhart I, Perkins L, Perrimon N, Mohr S. UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents. Genetics. 2013 Jun 21. PMID: 23792952.

UP-TORR, named for "Updated Targets of RNAi Reagents" checks daily for new updates to fly gene annotations and RNAi reagent collections (including TRiP, NIG-Japan and VDRC RNAi fly stocks). This lets you view the most updated interpretation of the gene-to-RNAi-reagent relationship.

Why does this matter? Because gene annotations change--sometimes a lot--over time, changing the interpretation of on-targets and off-targets of a reagent.

Please check out our paper to learn more. We also have a help page and a video demo online. As always, feedback on the online tool is welcome.

Breaking Report: Data Integration Tool

On my desk to read today? A paper describing a data integration tool that might be useful for analysis of RNAi screen data sets.

Renaud et al. (2012) DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. Nucleic Acids Res. PubMed ID: 22641854

Plate-to-List, List-to-Plate Conversion Tool

If you have ever copy-and-pasted data displayed like a 96- or 384-well plate to convert it to a simple list, or vice versa, then I expect you'll appreciate our newest online tool, the Plate-to-List, List-to-Plate conversion tool. It's designed for use with spreadsheets. We're finding it handy for some of our in-house stuff and expect it will be convenient for others as well. Big thanks to Ian Flockhart for developing the tool and getting it launched on the web very quickly!

DIOPT-DIST Updated

Our DIOPT-DIST tool was recently updated. Data from about 200 new GWAS studies was added. More info about the tool in the DIOPT paper and please feel free to ask us if you have questions.

DRSC's DIOPT and DIOPT-DIST

Sneak peak for blog readers: Our new ortholog-related tools DIOPT and DIOPT-DIST are available online and a provisional version of the paper describing the tools is also available at BMC Bioinformatics. As always, your feedback on our web-based tools is welcome!

Batch Search of TRiP Tools

Sneak peek for blog readers: here's a link to a batch search tool for TRiP stocks. Feedback welcome. It will be linked to from TRiP web pages on in vivo fly RNAi resources soon. Upload files should be .txt with one gene symbol (or other identifier) per line.

The DKFZ's GenomeRNAi turns 5.0

I just learned that the Boutros group at DKFZ has launched a "5.0" version of their GenomeRNAi database. Results from DRSC screens, other fly and mammalian cell-based screens, and fly in vivo screens are searchable at GenomeRNAi. Check it out!

Publications on GenomeRNAi are listed here.

Breaking Reports: Full-Genome RNAi on cell spreading & a Library Evaluation

On my desk today? Catching up on breaking reports from two different groups--one is a full-genome cell-based RNAi screen and the other a comparative report on genome-wide libraries.

D'Ambrosio & Vale (2010) A whole genome RNAi screen of Drosophila S2 cell spreading performed using automated computational image analysis. J Cell Bio 191(3):471-8. PMID: 21041442.

Horn et al. (2010) Design and evaluation of genome-wide libraries for RNA interference screens. Genome Biol. 11(6):R61. PMID 20550664.

Web Wednesday: RNAi Select

Following up on a recent post--breaking paper on dsRNA design--here's the link to the tool reported in the paper.

http://www.rnaiselect.info/dsrna/

Breaking Report: Limiting Off-Target Effects

Also on my desk today? An informatics analysis and tool for further limiting potential off-target effects in dsRNA design.

Seinen et al. (2010) RNAi Experiments in D. melanogaster: Solutions to the Overlooked Problem of Off-Targets Shared by Independent dsRNAs. PLoS One. 2010 Oct 1;5(10). pii: e13119.

Live Cell Imaging Analysis

What's on my desk today? A report on a new open source software package for analysis of high-throughput live cell images.

Held et al. (2010) CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nature Methods. 7, 747–754.

Web Wednesday: E-RNAi

A recent report in NAR describes an update to the E-RNAi tool for dsRNA design.

Horn & Boutros (2010) E-RNAi: a web application for the multi-species design of RNAi reagents—2010 update. Nucleic Acids Research. PMID: 20444868.

Web Wednesday: DRSC Gene LookUp ReDesign

We've revamped and added information at our Gene Lookup results page.

Search with a fly gene symbol or other ID, and get a report of what dsRNA amplicons we have for the gene (and if they've hit in screens), what TRiP in vivo RNAi lines we have for the gene, and--scroll to the very bottom--a sense of whether or not the gene is expressed in various cell lines, based on analysis of results from the modENCODE group.

Please check it out! Feedback welcome.

Web Wednesday: GenomeRNAi

Todays Web Wednesday featuer: GenomeRNAi, an effort from the Boutros group at DKFZ that reports an update in the most recent database issue of NAR:

Gilsdorf et al. (2009) GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. Nucleic Acids Res. doi: doi:10.1093/nar/gkp1038.

Database issue of NAR 2009 (free online access)

GenomeRNAi

And check out their "List all Screens" for what I assume is a summary of the screens that are searchable in the database. Included among the screens in Drosophila and human cells listed are many published screens based on data obtained at the DRSC. Looks like a good place to go to see what's out there from many groups.

Web Wednesday (well, Thurs)--Pathway Projector

Just learned about Pathway Projector, which describes itself as a zoomable interface for systems biology. Kono et al. (2009) Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API. PLoSOne (free on-line access).

Genetic Mapping

The Bloomington Drosophila Stock Center has announced availability of a Deficiency Kit. A great resource for the fly community!