Wednesday, June 26, 2013

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.

Tuesday, June 25, 2013

DKFZ announces version 11 of GenomeRNAi

The DKFZ recently announced launch of a version 11 of their meta-database of fly and human RNAi screen results, GenomeRNAi. Read their news item here.

Monday, June 10, 2013

Morphological complexity. Large-scale fly cell RNAi screen. Breaking report.

Data corresponding to the screen reported in this paper are available at and through PubChem. The fly cell screen was done in Kc cells. The study includes mammalian cell follow-up.

Yin et al. A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes. Nature Cell Biology (2013) doi:10.1038/ncb2764.

*See also* Olson MF. Finding the shape-shifter genes. Nat Cell Biol. 2013 PMID: 23817235.

piRNAs--genome-wide screen. Breaking report.

On my desk to read today? This report of an RNAi screen performed in ovarian somatic sheet cells.

Muerdter F, Guzzardo PM, Gillis J, Luo Y, Yu Y, Chen C, Fekete R, Hannon GJ. A Genome-wide RNAi Screen Draws a Genetic Framework for Transposon Control and Primary piRNA Biogenesis in Drosophila. Mol Cell. 2013 May 9. PMID: 23665228.

Friday, June 7, 2013

Differential RNAi and small libraries. Recent report.

Here's an example of a study that used two of the DRSC small libraries. These libraries have an optimal layout (limits edge effects) and average 2 or more unique dsRNAs per gene.

Garcia MA, Alvarez MS, Sailem H, Bousgouni V, Sero J, Bakal C. Differential RNAi screening provides insights into the rewiring of signalling networks during oxidative stress. Mol Biosyst. 2012 Oct;8(10):2605-13. PMID: 22790786.

New small library for cell-based RNAi screens: RNA binding proteins

For blog readers first: The DRSC recently created a new library for cell-based RNAi. The library targets RNA binding proteins. Average of 2 unique reagents per gene. Please contact the DRSC director for more info.

Monday, June 3, 2013

EDRC abstract deadline extended to June 12th

There's still to submit an abstract to the 23rd European Drosophila Research Conference. Just saw a notice that the abstract deadline was extended to June 12, 2013.

Catching up--RNAi screen for modifiers of disease-related toxicity

VoSSfeldt H, Butzlaff M, PrüSSing K, Ní Chárthaigh RA, Karsten P, Lankes A, Hamm S, Simons M, Adryan B, Schulz JB, Voigt A. Large-scale screen for modifiers of ataxin-3-derived polyglutamine-induced toxicity in Drosophila. PLoS One. 2012;7(11):e47452. PMID: 23139745; PMCID: PMC3489908.