Abstract
The Genitourinary Development Molecular Atlas Project (GUDMAP) aims to document gene expression across time and space in the developing urogenital system of the mouse, and to provide access to a variety of relevant practical and educational resources. Data come from microarray gene expression profiling (from laser-dissected and FACS-sorted samples) and in situ hybridization at both low (whole-mount) and high (section) resolutions. Data are annotated to a published, high-resolution anatomical ontology and can be accessed using a variety of search interfaces. Here, we explain how to run typical queries on the database, by gene or anatomical location, how to view data, how to perform complex queries, and how to submit data.
The online version of the original chapter can be found at http://dx.doi.org/10.1007/978-1-61779-851-1_36
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Little MH, Brennan J, Georgas K et al (2007) A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expr Patterns 7(6):680–699
Baldock RA, Bard JB, Burger A et al (2003) EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics 1:309–325
Brazma A, Hingamp P, Quackenbush J et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210
Deutsch EW, Ball CA, Berman JJ et al (2008) Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol 26:305–312
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Mugford JW, Yu J, Kobayashi A, McMahon AP (2009) High-resolution gene expression analysis of the developing mouse kidney defines novel cellular compartments within the nephron progenitor population. Dev Biol 333:312–323
Georgas K, Rumballe B, Wilkinson L et al (2008) Use of dual section mRNA in situ hybridisation/immunohistochemistry to clarify gene expression patterns during the early stages of nephron development in the embryo and in the mature nephron of the adult mouse kidney. Histochem Cell Biol 130:927–942
Brunskill EW, Aronow BJ, Georgas K et al (2008) Atlas of gene expression in the developing kidney at microanatomic resolution. Dev Cell 15:781–791
Georgas K, Rumballe B, Valerius MT et al (2009) Analysis of early nephron patterning reveals a role for distal RV proliferation in fusion to the ureteric tip via a cap mesenchyme-derived connecting segment. Dev Biol 332:273–286
Georgas KM, Chiu HS, Lesieur E, Rumballe BA, Little MH (2011) Expression of metanephric nephron-patterning genes in differentiating mesonephric tubules. Dev Dyn 240:1600–1612
Thiagarajan RD, Georgas KM, Rumballe BA et al (2011) Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. PLoS One 6:e17286
Chiu HS, Szucsik JC, Georgas KM et al (2010) Comparative gene expression analysis of genital tubercle development reveals a putative appendicular Wnt7 network for the epidermal differentiation. Dev Biol 344:1071–1087
Rolland AD, Lehmann KP, Johnson KJ, Gaido KW, Koopman P (2011) Uncovering gene regulatory networks during mouse fetal germ cell development. Biol Reprod 84:790–800
Acknowledgements
The GUDMAP database is funded by the National Institute of Digestion, Diabetes, and Kidney Disease (NIDDK), NIH, and the National Institute of Child Health and Human Development.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Davies, J.A. et al. (2012). Access and Use of the GUDMAP Database of Genitourinary Development. In: Michos, O. (eds) Kidney Development. Methods in Molecular Biology™, vol 886. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-851-1_17
Download citation
DOI: https://doi.org/10.1007/978-1-61779-851-1_17
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-850-4
Online ISBN: 978-1-61779-851-1
eBook Packages: Springer Protocols