Comparative, transcriptome analysis of self-organizing optic tissues

Scientific Data

Volumn 2, Issue , 2015, Pages

  Andrabi, Munazah ^a   Kuraku, Shigehiro ^a   Takata, Nozomu ^b   Sasai, Yoshiki ^b   Love, Nick R ^b  

^a RIKEN   (Japan)

^b RIKEN Center for Biosystems Dynamics Research   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

FIBROBLAST GROWTH FACTOR; TRANSCRIPTOME;

ANIMAL; CELL CULTURE TECHNIQUE; CELL DIFFERENTIATION; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; RETINA; RETINAL PIGMENT EPITHELIUM; WNT SIGNALING PATHWAY;

ANIMALS; CELL CULTURE TECHNIQUES; CELL DIFFERENTIATION; FIBROBLAST GROWTH FACTORS; GENE EXPRESSION PROFILING; RETINA; RETINAL PIGMENT EPITHELIUM; TRANSCRIPTOME; WNT SIGNALING PATHWAY;

EID: 84960955597     PISSN: None     EISSN: 20524463     Source Type: Journal    
DOI: 10.1038/sdata.2015.30     Document Type: Article

References (39)

1. Fuhrmann, S. Eye morphogenesis and patterning of the optic vesicle. Curr. Top. Dev. Biol. 93, 61-84 (2010).
2. Livesey, F. J. & Cepko, C. L. Vertebrate neural cell-fate determination: lessons from the retina. Nat. Rev. Neurosci. 2, 109-118 (2001).
3. Rowan, S., Chen, C. M., Young, T. L., Fisher, D. E. & Cepko, C. L. Transdifferentiation of the retina into pigmented cells in ocular retardation mice defines a new function of the homeodomain gene Chx10. Development 131, 5139-5152 (2004).
4. Sasai, Y. Cytosystems dynamics in self-organization of tissue architecture. Nature 493, 318-326 (2013).
5. Sasai, Y., Eiraku, M. & Suga, H. In vitro organogenesis in three dimensions: self-organising stem cells. Development 139, 4111-4121 (2012).
6. Wataya, T. et al. Minimization of exogenous signals in ES cell culture induces rostral hypothalamic differentiation. Proc. Natl Acad. Sci. USA 105, 11796-11801 (2008).
7. Eiraku, M. et al. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 472, 51-56 (2011).
8. Aoki, H. et al. Embryonic stem cells that differentiate into RPE cell precursors in vitro develop into RPE cell monolayers in vivo. Exp. Eye Res. 82, 265-274 (2006).
9. Fuhrmann, S. Wnt signaling in eye organogenesis. Organogenesis 4, 60-67 (2008).
10. Fujimura, N., Taketo, M. M., Mori, M., Korinek, V. & Kozmik, Z. Spatial and temporal regulation of Wnt/beta-catenin signaling is essential for development of the retinal pigment epithelium. Dev. Biol. 334, 31-45 (2009).
11. Guillemot, F. & Cepko, C. L. Retinal fate and ganglion cell differentiation are potentiated by acidic FGF in an in vitro assay of early retinal development. Development 114, 743-754 (1992).
12. Hyer, J., Mima, T. & Mikawa, T. FGF1 patterns the optic vesicle by directing the placement of the neural retina domain. Development 125, 869-877 (1998).
13. Pittack, C., Grunwald, G. B. & Reh, T. A. Fibroblast growth factors are necessary for neural retina but not pigmented epithelium differentiation in chick embryos. Development 124, 805-816 (1997).
14. Westenskow, P., Piccolo, S. & Fuhrmann, S. Beta-catenin controls differentiation of the retinal pigment epithelium in the mouse optic cup by regulating Mitf and Otx2 expression. Development 136, 2505-2510 (2009).
15. Dorsky, R. I., Sheldahl, L. C. & Moon, R. T. A transgenic Lef1/beta-catenin-dependent reporter is expressed in spatially restricted domains throughout zebrafish development. Dev. Biol. 241, 229-237 (2002).
16. Murray, J. T. et al. Exploitation of KESTREL to identify NDRG family members as physiological substrates for SGK1 and GSK3. Biochem. J 384, 477-488 (2004).
17. Xiang, M. et al. The Brn-3 family of POU-domain factors: primary structure, binding specificity, and expression in subsets of retinal ganglion cells and somatosensory neurons. J. Neurosci. 15, 4762-4785 (1995).
18. Xiang, M. Requirement for Brn-3b in early differentiation of postmitotic retinal ganglion cell precursors. Dev. Biol. 197, 155-169 (1998).
19. Haruta, M. et al. In vitro and in vivo characterization of pigment epithelial cells differentiated from primate embryonic stem cells. Invest. Ophthalmol. Vis. Sci. 45, 1020-1025 (2004).
20. Kamao, H. et al. Characterization of human induced pluripotent stem cell-derived retinal pigment epithelium cell sheets aiming for clinical application. Stem Cell Reports 2, 205-218 (2014).
21. Kanemura, H. et al. Tumorigenicity studies of induced pluripotent stem cell (iPSC)-derived retinal pigment epithelium (RPE) for the treatment of age-related macular degeneration. PLoS ONE 9, e85336 (2014).
22. Eiraku, M. & Sasai, Y. Mouse embryonic stem cell culture for generation of three-dimensional retinal and cortical tissues. Nat. Protoc. 7, 69-79 (2012).
23. Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519-523 (2008).
24. Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590-604 (2012).
25. Eiraku, M. et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3, 519-532 (2008).
26. Ikeda, H. et al. Generation of Rx+/Pax6+ neural retinal precursors from embryonic stem cells. Proc. Natl Acad. Sci. USA 102, 11331-11336 (2005).
27. Andrews, S. FastQC: A quality control tool for high throughput sequence data, http://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ (2010).
28. Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
29. Goecks, J., Eberhard, C., Too, T., Nekrutenko, A. & Taylor, J. Web-based visual analysis for high-throughput genomics. BMC Genomics 14, 397 (2013).
30. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
31. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
32. Jho, E. H. et al. Wnt/beta-catenin/Tcf signaling induces the transcription of Axin2, a negative regulator of the signaling pathway. Mol. Cell. Biol. 22, 1172-1183 (2002).
33. Bell, S. M. et al. R-spondin 2 is required for normal laryngeal-tracheal, lung and limb morphogenesis. Development 135, 1049-1058 (2008).
34. Braun, M. M., Etheridge, A., Bernard, A., Robertson, C. P. & Roelink, H. Wnt signaling is required at distinct stages of development for the induction of the posterior forebrain. Development 130, 5579-5587 (2003).
35. Furukawa, T., Morrow, E. M. & Cepko, C. L. Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation. Cell 91, 531-541 (1997).
36. Barbieri, A. M. et al. A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. Proc. Natl Acad. Sci. USA 96, 10729-10734 (1999).
37. Sivak, J. M., Petersen, L. F. & Amaya, E. FGF signal interpretation is directed by Sprouty and Spred proteins during mesoderm formation. Dev. Cell 8, 689-701 (2005).
38. Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8, 1765-1786 (2013).
39. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).