Title	Journal	Author(s)	Aniseed Data	PMID/DOI
Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.	PLoS Biol. 2013; 11; 10:e1001697	Katikala L, Aihara H, Passamaneck Y, Gazdoiu S, José-Edwards D, Kugler J, Oda-Ishii I, Imai J, Nibu Y, Di Gregorio A
Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development.	Development 2013; 140; 11:2422-33	José-Edwards D, Oda-Ishii I, Nibu Y, Di Gregorio A
Guidelines for the nomenclature of genetic elements in tunicate genomes.	Genesis 2015; 53; 1:1-14	Stolfi A, Sasakura Y, Chalopin D, Satou Y, Christiaen L, Dantec C, Endo T, Naville M, Nishida H, Swalla B, Volff J, Voskoboynik A, Dauga D, Lemaire P
β-Catenin-driven binary fate specification segregates germ layers in ascidian embryos.	Curr. Biol. 2013; 23; 6:491-5	Hudson C, Kawai N, Negishi T, Yasuo H
Characterization of Brachyury-downstream notochord genes in the Ciona intestinalis embryo.	Dev. Biol. 2000; 224; 1:69-80	Hotta K, Takahashi H, Asakura T, Saitoh B, Takatori N, Satou Y, Satoh N
Ephrin signaling establishes asymmetric cell fates in an endomesoderm lineage of the Ciona embryo.	Development 2008; 135; 5:931-40	Shi W, Levine M
Auto and cross regulatory elements control Onecut expression in the ascidian nervous system.	Dev. Biol. 2014; 390; 2:273-87	Pezzotti M, Locascio A, Racioppi C, Fucci L, Branno M
p120RasGAP mediates ephrin/Eph-dependent attenuation of FGF/ERK signals during cell fate specification in ascidian embryos.	Development 2013; 140; 21:4347-52	Haupaix N, Stolfi A, Sirour C, Picco V, Levine M, Christiaen L, Yasuo H
FGF8/17/18 functions together with FGF9/16/20 during formation of the notochord in Ciona embryos.	Dev. Biol. 2007; 302; 1:92-103	Yasuo H, Hudson C
Gene expression profiles in Ciona intestinalis cleavage-stage embryos.	Mech. Dev. 2002; 112; 1-2:115-27	Fujiwara S, Maeda Y, Shin-I T, Kohara Y, Takatori N, Satou Y, Satoh N
A conserved role for the MEK signalling pathway in neural tissue specification and posteriorisation in the invertebrate chordate, the ascidian Ciona intestinalis.	Development 2003; 130; 1:147-59	Hudson C, Darras S, Caillol D, Yasuo H, Lemaire P
Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis.	Development 2003; 130; 26:6485-95	Yamada L, Shoguchi E, Wada S, Kobayashi K, Mochizuki Y, Satou Y, Satoh N
A zinc finger transcription factor, ZicL, is a direct activator of Brachyury in the notochord specification of Ciona intestinalis.	Development 2004; 131; 6:1279-88	Yagi K, Satou Y, Satoh N
Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks.	Development 2004; 131; 16:4047-58	Imai K, Hino K, Yagi K, Satoh N, Satou Y
Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis.	Development 1997; 124; 3:589-602	Corbo J, Levine M, Zeller R
Lineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochord.	Dev. Dyn. 2007; 236; 7:1806-19	Oda-Ishii and Di Gregorio
Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis.	Genesis 2008; 46; 11:697-710	Kugler J, Passamaneck Y, Feldman T, Beh J, Regnier T, Di Gregorio A
Regulatory blueprint for a chordate embryo.	Science 2006; 312; 5777:1183-7	Imai K, Levine M, Satoh N, Satou Y
A signalling relay involving Nodal and Delta ligands acts during secondary notochord induction in Ciona embryos.	Development 2006; 133; 15:2855-64	Hudson C, Yasuo H
Ephrin-Eph signalling drives the asymmetric division of notochord/neural precursors in Ciona embryos.	Development 2007; 134; 8:1491-7	Picco V, Hudson C, Yasuo H
Differential temporal control of Foxa.a and Zic-r.b specifies brain versus notochord fate in the ascidian embryo.	Development 2017; 144; 1:38-43	Ikeda T, Satou Y
Co-expression of Foxa.a, Foxd and Fgf9/16/20 defines a transient mesendoderm regulatory state in ascidian embryos.	Elife 2016; 5; :	Hudson C, Sirour C, Yasuo H
Differential gene expression in notochord and nerve cord fate segregation in the Ciona intestinalis embryo.	Genesis 2013; 51; 9:647-59	Kobayashi K, Yamada L, Satou Y, Satoh N
A Nodal/Eph signalling relay drives the transition from apical constriction to apico-basal shortening in ascidian endoderm invagination.	Development 2020; 147; 15:	Fiuza U, Negishi T, Rouan A, Yasuo H, Lemaire P
Brachyury null mutant-induced defects in juvenile ascidian endodermal organs.	Development 2009; 136; 1:35-9	Chiba S, Jiang D, Satoh N, Smith W
FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.	Development 2009; 136; 1:23-8	Shi W, Peyrot S, Munro E, Levine M
The snail repressor establishes a muscle/notochord boundary in the Ciona embryo.	Development 1998; 125; 13:2511-20	Fujiwara S, Corbo J, Levine M
M-Ras evolved independently of R-Ras and its neural function is conserved between mammalian and ascidian, which lacks classical Ras.	Gene 2009; 429; 1-2:49-58	Keduka E, Kaiho A, Hamada M, Watanabe-Takano H, Takano K, Ogasawara M, Satou Y, Satoh N, Endo T
Neural tissue in ascidian embryos is induced by FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors.	Cell 2003; 115; 5:615-27	Bertrand V, Hudson C, Caillol D, Popovici C, Lemaire P
Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis.	Development 2009; 136; 21:3679-89	Passamaneck Y, Katikala L, Perrone L, Dunn M, Oda-Ishii I, Di Gregorio A
Ci-Rga, a gene encoding an MtN3/saliva family transmembrane protein, is essential for tissue differentiation during embryogenesis of the ascidian Ciona intestinalis.	Differentiation 2005; 73; 7:364-76	Hamada M, Wada S, Kobayashi K, Satoh N
Suppressor of hairless activates brachyury expression in the Ciona embryo.	Dev. Biol. 1998; 203; 2:358-68	Corbo J, Fujiwara S, Levine M, Di Gregorio A
Interaction of notochord-derived fibrinogen-like protein with Notch regulates the patterning of the central nervous system of Ciona intestinalis embryos.	Dev. Biol. 2009; 328; 1:1-12	Yamada S, Hotta K, Yamamoto T, Ueno N, Satoh N, Takahashi H
Brachyury downstream notochord differentiation in the ascidian embryo.	Genes Dev. 1999; 13; 12:1519-23	Takahashi H, Hotta K, Erives A, Di Gregorio A, Zeller R, Levine M, Satoh N