Clone Mapper: An Online Suite of Tools for RNAi Experiments in Caenorhabditis elegans

Abstract

RNA interference (RNAi), mediated by the introduction of a specific double-stranded RNA, is a powerful method to investigate gene function. It is widely used in the Caenorhabditis elegans research community. An expanding number of laboratories conduct genome-wide RNAi screens, using standard libraries of bacterial clones each designed to produce a specific double-stranded RNA. Proper interpretation of results from RNAi experiments requires a series of analytical steps, from the verification of the identity of bacterial clones, to the identification of the clones’ potential targets. Despite the popularity of the technique, no user-friendly set of tools allowing these steps to be carried out accurately, automatically, and at a large scale, is currently available. We report here the design and production of Clone Mapper, an online suite of tools specifically adapted to the analysis pipeline typical for RNAi experiments with C. elegans. We show that Clone Mapper overcomes the limitations of existing techniques and provide examples illustrating its potential for the identification of biologically relevant genes. The Clone Mapper tools are freely available via http://www.ciml.univ-mrs.fr/EWBANK_jonathan/software.html.

A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes

“…We then used a simple cut-off to classify 28 clones as being capable of causing a strong Hipi phenotype (termed, “Hipi clones”; Additional file 3 : Table S3). We used sequencing and Clone Mapper [ 28 ] to verify the identity of the Hipi clones and determine their putative target genes (Additional file 3 : Table S3). These included bus-2 and bus-12 , which respectively encode a galactosyltransferase and a sugar transporter required for the post-translational modification of surface-exposed proteins [ 29 , 30 ].…”

“…An alternative is to undertake automated quantitative screens. These require specialized equipment and tools for data storage and analysis [ 18 , 19 , 28 , 79 – 82 ] and are thus more difficult to put in place. Further, they also suffer from the intrinsic variability of RNAi, which cannot be adequately accounted for using formal statistical analyses (Thomas Richardson, University of Washington, personal communication).…”

Microtubule plus-end dynamics link wound repair to the innate immune response

“…The RNAi bacterial clones were obtained from the Ahringer library (Kamath et al, 2003) or Vidal library (Rual et al, 2004) and sequenced to confirm their identity using CloneMapper (Thakur et al, 2014…”

Evolutionary plasticity in the innate immune function of Akirin

“…RNAi clones were from the Ahringer (Kamath, Fraser et al, 2003) and the Vidal (Rual, Ceron et al, 2004) RNAi libraries. Insert sequences were verified and target genes confirmed using Clone Mapper (Thakur, Pujol et al, 2014) before use. Epidermal-specific RNAi used the strain IG1502 rde-1(ne219);Is ;frIs7 [nlp-29p::gfp, col-12p::DsRed] (Zugasti et al, 2014).…”