The transgenic RNAi project at Harvard medical school: Resources and validation

Genetics

Volumn 201, Issue 3, 2015, Pages 843-852

  Perkins, Lizabeth A ^a   Holderbaum, Laura ^a   Tao, Rong ^a   Hu, Yanhui ^a   Sopko, Richelle ^a   McCall, Kim ^b   Yang Zhou, Donghui ^a   Flockhart, Ian ^a   Binari, Richard ^a,c   Shim, Hye Seok ^a   Miller, Audrey ^a   Housden, Amy ^a   Foos, Marianna ^a   Randkelv, Sakara ^a   Kelley, Colleen ^a   Namgyal, Pema ^a   Villalta, Christians ^a,c   Liu, Lu Ping ^a,d   Jiang, Xia ^d   Huan Huan, Qiao ^d   Wang, Xia ^d   Fujiyama, Asao ^e   Toyoda, Atsushi ^e   Ayers, Kathleen ⁱ   Blum, Allison ^c,f   Czech, Benjamin ^g   Neumuller, Ralph ^a   Yan, Dong ^a   Cavallaro, Amanda ^c,h   Hibbard, Karen ^c,h   Hall, Don ^c,h   Cooley, Lynn ⁱ   Hannon, Gregory J ^g   Lehmann, Ruth ^c,f   Parks, Annette ^j   Mohr, Stephanie E ^a   Ueda, Ryu ^e   Kondo, Shu ^a,e   Ni, Jian Quan ^a,d   Perrimon, Norbert ^a,c   more..

^a HARVARD MEDICAL SCHOOL   (United States)

^b BOSTON UNIVERSITY   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d TSINGHUA UNIVERSITY   (China)

^e NATIONAL INSTITUTE OF GENETICS   (Japan)

^f NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^h Janelia Farm   (United States)

ⁱ YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^j Bloomington Drosophila Stock Center   (United States)

more..

Author keywords

Drosophila; Functional genomics; Phenotypes; RNAi; Screens

Indexed keywords

DIAZEPAM; DOUBLE STRANDED RNA; MERCURY SULFIDE; REAGENT; SHORT HAIRPIN RNA;

ARTICLE; DROSOPHILA; FOSMID; GENE DOSAGE; GENE OVEREXPRESSION; GENE SILENCING; GENE VECTOR; GENOTYPE; LOXP SITE; NONHUMAN; ONLINE SYSTEM; ORTHOLOGY; OVARY FOLLICLE CELL; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA VECTOR; TRANSGENE; WILD TYPE; ACCESS TO INFORMATION; ANIMAL; GENE; GENETICS; MASSACHUSETTS; MEDICAL RESEARCH; MEDICAL SCHOOL; TRANSGENIC ANIMAL; VALIDATION STUDY;

ACCESS TO INFORMATION; ANIMALS; ANIMALS, GENETICALLY MODIFIED; BIOMEDICAL RESEARCH; BOSTON; DROSOPHILA; GENES, INSECT; GENETIC VECTORS; RNA INTERFERENCE; SCHOOLS, MEDICAL;

EID: 84946596732     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.180208     Document Type: Article

References (23)

1. An, X., J. D. Armstrong, K. Kaiser, and K. M. O'Dell, 2000 The effects of ectopic white and transformer expression on Drosophila courtship behavior. J. Neurogenet. 14: 227-243, 271.
2. Buehler, E., Y. C. Chen, and S. Martin, 2012 C911: a bench-level control for sequence specific siRNA off-target effects. PLoS One 7: e51942.
3. Dietzl, G., D. Chen, F. Schnorrer, K. C. Su, Y. Barinova et al., 2007 A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448: 151-156.
4. Flockhart, I. T., M. Booker, Y. Hu, B. McElvany, Q. Gilly et al., 2012 FlyRNAi.org: the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res. 40: D715-D719.
5. Groth, A. C., M. Fish, R. Nusse, and M. P. Calos, 2004 Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics 166: 1775-1782.
6. Hu, Y., I. Flockhart, A. Vinayagam, C. Bergwitz, B. Berger et al., 2011 An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 12: 357.
7. Hu, Y., C. Roesel, I. Flockhart, L. Perkins, N. Perrimon, and S.E. Mohr 2013a UP-TORR:online tool for accurate and up-to-date annotation of RNAi reagents. Genetics 195: 37-45.
8. Hu, Y., R. Sopko, M. Foos, C. Kelley, I. Flockhart et al., 2013b FlyPrimerBank: an online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents. G3 Genes Genomes Genet. 3: 1607-1616.
9. Hu, Y., A. Comjean, L. A. Perkins, N. Perrimon, and S. E. Mohr, 2015 GLAD: an Online Database of Gene List Annotation for Drosophila. J Genomics 3: 75-81.
10. Kondo, S.,M. Booker, and N. Perrimon, 2009 Cross-species RNAi rescue platform in Drosophila melanogaster. Genetics 183: 1165-1173.
11. Langer, C. C., R. K. Ejsmont, C. Schonbauer, F. Schnorrer, and P. Tomancak, 2010 In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura. PLoS One 5: e8928.
12. Liu, N., and P. Lasko, 2015 Analysis of RNA interference lines identifies new functions of maternally-expressed genes involved in embryonic patterning in Drosophila melanogaster. G3 (Bethesda). 5: 1025-34.
13. Markstein, M., C. Pitsouli, C. Villalta, S. E. Celniker, and N. Perrimon, 2008 Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat. Genet. 40: 476-483.
14. Ni, J. Q., M. Markstein, R. Binari, B. Pfeiffer, L. P. Liu et al., 2008 Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster. Nat. Methods 5: 49-51.
15. Ni, J. Q., L. P. Liu, R. Binari, R. Hardy, H. S. Shim et al., 2009 A Drosophila resource of transgenic RNAi lines for neurogenetics. Genetics 182: 1089-1100.
16. Ni, J. Q., R. Zhou, B. Czech, L. P. Liu, L. Holderbaum et al., 2011 A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat. Methods. 8(5): 405-7.
17. Perrimon, N., J. Q. Ni, and L. Perkins, 2010 In vivo RNAi: today and tomorrow. Cold Spring Harb. Perspect. Biol. 2: a003640.
18. Potter, C. J., B. Tasic, E. V. Russler, L. Liang, and L. Luo, 2010 The Q system: a repressible binary system for transgene expression, lineage tracing, and mosaic analysis. Cell 141: 536-548.
19. Sopko, R., M. Foos, A. Vinayagam, B. Zhai, R. Binari et al., 2014 Combining genetic perturbations and proteomics to examine kinase-phosphatase networks in Drosophila embryos. Dev. Cell 31: 114-127.
20. Staller, M. V., D. Yan, S. Randklev, M. D. Bragdon, Z. B.Wunderlich et al., 2013 Depleting gene activities in early Drosophila embryos with the "maternal-Gal4-shRNA" system. Genetics 193: 51-61.
21. Vert, J. P., N. Foveau, C. Lajaunie, and Y. Vandenbrouck, 2006 An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics 7: 520.
22. Yan, D., R. A. Neumuller, M. Buckner, K. Ayers, H. Li et al., 2014 A regulatory network of Drosophila germline stem cell selfrenewal. Dev. Cell 28: 459-473.
23. Zeng, X., L. Han, S. R. Singh, H. Liu, R. A. Neumuller et al., 2015 Genome-wide RNAi screen identifies networks involved in intestinal stem cell regulation in Drosophila. Cell Reports 10: 1226-1238.