GEISHA: an evolving gene expression resource for the chicken embryo

Antin, Parker B.; Yatskievych, Tatiana A.; Davey, Sean; Darnell, Diana K.

doi:10.1093/nar/gkt962

Cited by 78 publications

(98 citation statements)

References 12 publications

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“…We continue to maintain links to mouse expression data from the Allen Institute (13), GENSAT (14), GEO (15) and EBI's Expression Atlas (16). We have added links to expression data from other vertebrate model organisms highly relevant for developmental research: zebrafish (ZFIN, 17), Xenopus (Xenbase, 18) and chicken (GEISHA, 19). …”

Section: Enhancements Of Data Structure and Web Interfacementioning

confidence: 99%

The mouse Gene Expression Database (GXD): 2017 update

et al. 2016

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The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissue-by-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species.

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Section: Enhancements Of Data Structure and Web Interfacementioning

confidence: 99%

The mouse Gene Expression Database (GXD): 2017 update

et al. 2016

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“…The most likely ligands involved in this step are FGF2, FGF8 and/or FGF9, all of which are expressed in the mesonephric region, and are known to have high affinity for FGFR2 (Antin et al, 2014;Martin et al, 2006;Yoshioka et al, 2005). Our study has also revealed that FGF signaling in the MFR is intracellularly transduced through the Ras/ERK pathway but not the PI3K/AKT pathway ( Fig.…”

Section: Discussionmentioning

confidence: 51%

Early formation of the Müllerian duct is regulated by sequential actions of BMP/Pax2 and FGF/Lim1 signaling

Atsuta

Takahashi

2016

Development

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The Müllerian duct (MD) and Wolffian duct (WD) are embryonic tubular tissues giving rise to female and male reproductive tracts, respectively. In amniote embryos, both MD and WD emerge in both sexes, but subsequently degenerate in the males and females, respectively. Here, by using MD-specific gene manipulations in chicken embryos, we identify the molecular and cellular mechanisms that link early MD specification to tubular invagination. Early ( pre-) specification of MD precursors in the coelomic epithelium requires BMP signaling and its downstream target Pax2 in a WD-independent process. Subsequently, the BMP/Pax2 axis induces Lim1 expression, a hallmark of MD specification, for which FGF/ERK and WD-derived signals are also required. Finally, the sequential actions of the BMP/Pax2 and FGF/Lim1 axes culminate in epithelial invagination to form a tubular structure driven by an apical constriction, where apical accumulation of phospho-myosin light chain is positively regulated by FGF/ERK signaling. Our study delineates mechanisms governing the early formation of the MD, and also serves as a model of how an epithelial cell sheet is transformed to a tubular structure, a process seen in a variety of developmental contexts.

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“…For example, databases such as those hosted by the University of Arizona (Geisha) (Antin et al, 2013; Bell et al, 2004), provide powerful resources for the pattern of gene expression during embryogenesis. Furthermore, the advent of next generation sequencing technologies such as dSAGE and RNAseq provide whole transcriptome quantification and profiling not previously available for studies in avians.…”

Section: Methods: Techniques For Handling the Embryomentioning

confidence: 99%

Avians as a Model System of Vascular Development

Bressan

Matsukawa

2014

Methods in Molecular Biology

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Summary For more then 2000 years philosophers and scientists have turned to the avian embryo with questions of how life begins (Aristotle; Needham, 1959). Then, as now, the unique accessibility of the embryo both in terms of acquisition of eggs from domesticated fowl, and ease at which the embryo can be visualized by simply opening the shell, have made avians an appealing and powerful model system for the study of development. Thus, as the field of embryology has evolved through observational, comparative, and experimental embryology, into its current iteration as the cellular and molecular biology of development, avians have remained a useful and practical system of study.

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GEISHA: an evolving gene expression resource for the chicken embryo

Cited by 78 publications

References 12 publications

The mouse Gene Expression Database (GXD): 2017 update

The mouse Gene Expression Database (GXD): 2017 update

Early formation of the Müllerian duct is regulated by sequential actions of BMP/Pax2 and FGF/Lim1 signaling

Avians as a Model System of Vascular Development

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