An analysis and validation pipeline for large-scale RNAi-based screens

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Plank, Michael ^a   Hu, Guang ^b   Sofia Silva, A ^a,d   Wood, Shona H ^a   Hesketh, Emily E ^a   Janssens, Georges ^a,e   MacEdo, André ^a   De Magalhães, João Pedro ^a   Church, George M ^c  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF BEIRA INTERIOR   (Portugal)

^e UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOCYANINE; CYANINE DYE 3; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; CHEMISTRY; DNA MICROARRAY; EMBRYONIC STEM CELL; GENETICS; METABOLISM; MOUSE; OXIDATIVE STRESS; RNA INTERFERENCE;

ANIMALS; CARBOCYANINES; EMBRYONIC STEM CELLS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATIVE STRESS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

MLCS; MLOWN;

EID: 84872699671     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01076     Document Type: Article

References (39)

1. Shenghui, H., Nakada, D. &Morrison, S. J. Mechanisms of stem cell self-renewal. Annual Review of Cell and Developmental Biology 25, 377-406 (2009).
2. Verfaillie, C. M. Adult stem cells: assessing the case for pluripotency. Trends Cell Biol 12, 502-8 (2002). (Pubitemid 35346700)
3. Nijnik, A. et al. DNA repair is limiting for haematopoietic stem cells during ageing. Nature 447, 686-690 (2007). (Pubitemid 46889732)
4. Maslov, A. Y., Barone, T. A., Plunkett, R. J. & Pruitt, S. C. Neural stem cell detection, characterization, and age-related changes in the subventricular zone of mice. J Neurosci 24, 1726-33 (2004). (Pubitemid 38240970)
5. de Magalhaes, J. P. & Faragher, R. G. Cell divisions and mammalian aging: integrative biology insights from genes that regulate longevity. Bioessays 30, 567-78 (2008). (Pubitemid 351859413)
6. Kaeberlein, M. Molecular basis of ageing. EMBO reports 8, 907-911 (2007). (Pubitemid 47500471)
7. Zeng, X.&Rao, M. S. Human embryonic stem cells: Long term stability, absence of senescence and a potential cell source for neural replacement. Neuroscience 145, 1348-1358 (2007). (Pubitemid 46602730)
8. Freitas, A. A. & de Magalhaes, J. P. A review and appraisal of the DNA damage theory of ageing. Mutat Res 728, 12-22 (2011).
9. Pan, G. & Thomson, J. A. Nanog and transcriptional networks in embryonic stem cell pluripotency. Cell research 17, 42-49 (2007). (Pubitemid 46096423)
10. Shen, S. W. & Song, H. Y. Progesterone promotes propagation and viability of mouse embryonic stem cells. Sheng li xue bao : [Acta physiologica Sinica] 61, 431-438 (2009).
11. Moscatelli, I., Pierantozzi, E., Camaioni, A., Siracusa, G. & Campagnolo, L. p75 neurotrophin receptor is involved in proliferation of undifferentiated mouse embryonic stem cells. Experimental Cell Research 315, 3220-3232 (2009).
12. Hu, G. et al. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes & development 23, 837-848 (2009).
13. Boheler, K. R. Stem cell pluripotency: a cellular trait that depends on transcription factors, chromatin state and a checkpoint deficient cell cycle. Journal of cellular physiology 221, 10-17 (2009).
14. Liu, N., Lu, M., Tian, X.&Han, Z. Molecular mechanisms involved in self-renewal and pluripotency of embryonic stem cells. Journal of cellular physiology 211, 279-286 (2007). (Pubitemid 46580081)
15. Johnson, T. E., Lithgow, G. J. & Murakami, S. Hypothesis: interventions that increase the response to stress offer the potential for effective life prolongation and increased health. J Gerontol A Biol Sci Med Sci 51, B392-5 (1996). (Pubitemid 26394064)
16. Harper, J. M., Salmon, A. B., Leiser, S. F., Galecki, A. T. & Miller, R. A. Skinderived fibroblasts from long-lived species are resistant to some, but not all, lethal stresses and to the mitochondrial inhibitor rotenone. Aging Cell 6, 1-13 (2007). (Pubitemid 46140135)
17. Kim, Y. & Sun, H. Functional genomic approach to identify novel genes involved in the regulation of oxidative stress resistance and animal lifespan. Aging Cell 6, 489-503 (2007). (Pubitemid 47087054)
18. Schlabach, M. R. et al. Cancer proliferation gene discovery through functional genomics. Science 319, 620-4 (2008). (Pubitemid 351197064)
19. Echeverri, C. J.&Perrimon, N. High-throughput RNAi screening in cultured cells: a user's guide. Nature reviews.Genetics 7, 373-384 (2006).
20. Silva, J. M. et al. Second-generation shRNA libraries covering the mouse and human genomes. Nature genetics 37, 1281-1288 (2005). (Pubitemid 41568714)
21. Moffat, J. & Sabatini, D. M. Building mammalian signalling pathways with RNAi screens. Nat Rev Mol Cell Biol 7, 177-87 (2006).
22. Tu, Z. et al. Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network. Genome Res 19, 1057-67 (2009).
23. Chang, K., Elledge, S. J. & Hannon, G. J. Lessons from Nature: microRNA-based shRNA libraries. Nat Methods 3, 707-14 (2006). (Pubitemid 44275738)
24. Dennis, G., Jr. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4, P3 (2003).
25. Su, H. et al. Mammalian hyperplastic discs homolog EDD regulates miRNAmediated gene silencing. Mol Cell 43, 97-109 (2011).
26. Smogorzewska, A. et al. Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell 129, 289-301 (2007). (Pubitemid 46584733)
27. Ivanova, N. et al. Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533-8 (2006). (Pubitemid 44167907)
28. Henderson,M. J. et al. EDD mediates DNA damage-induced activation of CHK2. J Biol Chem 281, 39990-40000 (2006). (Pubitemid 46041803)
29. Munoz, M. A. et al. The E3 ubiquitin ligase EDD regulates S-phase and G(2)/M DNA damage checkpoints. Cell Cycle 6, 3070-7 (2007).
30. Saunders, D. N. et al. Edd, the murine hyperplastic disc gene, is essential for yolk sac vascularization and chorioallantoic fusion. Mol Cell Biol 24, 7225-34 (2004). (Pubitemid 39014448)
31. Pan, H., Mostoslavsky, G., Eruslanov, E., Kotton, D. N. & Kramnik, I. Dualpromoter lentiviral system allows inducible expression of noxious proteins in macrophages. J Immunol Methods 329, 31-44 (2008). (Pubitemid 350235459)
32. Sena-Esteves, M., Saeki, Y., Camp, S. M., Chiocca, E. A. & Breakefield, X. O. Single-step conversion of cells to retrovirus vector producers with herpes simplex virus-Epstein-Barr virus hybrid amplicons. J Virol 73, 10426-39 (1999).
33. Robertson, E., Bradley, A., Kuehn, M. & Evans, M. Germ-line transmission of genes introduced into cultured pluripotential cells by retroviral vector. Nature 323, 445-8 (1986). (Pubitemid 16026271)
34. de Magalhaes, J. P., Chainiaux, F., Remacle, J. & Toussaint, O. Stress-induced premature senescence in BJ and hTERT-BJ1 human foreskin fibroblasts. FEBS Lett 523, 157-62 (2002). (Pubitemid 34786078)
35. Guo, Y. L., Chakraborty, S., Rajan, S. S., Wang, R. & Huang, F. Effects of oxidative stress on mouse embryonic stem cell proliferation, apoptosis, senescence, and selfrenewal. Stem Cells Dev 19, 1321-31 (2010).
36. de Magalhaes, J. P., Curado, J. & Church, G. M. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 25, 875-81 (2009).
37. Hailesellasse Sene, K. et al. Gene function in early mouse embryonic stem cell differentiation. BMC Genomics 8, 85 (2007).
38. Marshall, O. J. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20, 2471-2 (2004). (Pubitemid 39429922)
39. Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402-8 (2001). (Pubitemid 34164012)