A high-resolution anatomical atlas of the transcriptome in the mouse embryo.

Graciana Diez-Roux 1 Sandro Banfi 1 Marc Sultan 2 Lars Geffers 3 Santosh Anand 1 David Rozado 2 Alon Magen 2 Elena Canidio 4 Massimiliano Pagani 4 Ivana Peluso 1 Nathalie Lin-Marq 5 Muriel Koch 6 Marchesa Bilio 1 Immacolata Cantiello 1 Roberta Verde 1 Cristian de Masi 1 Salvatore Bianchi 1 Juliette Cicchini 5 Elodie Perroud 5 Shprese Mehmeti 5 Emilie Dagand 2 Sabine Schrinner 2 Asja Nürnberger 2 Katja Schmidt 2 Katja Metz 2 Christina Zwingmann 2 Norbert Brieske 2 Cindy Springer 2 Ana Martinez Hernandez 3 Sarah Herzog 3 Frauke Grabbe 3 Cornelia Sieverding 3 Barbara Fischer 3 Kathrin Schrader 3 Maren Brockmeyer 3 Sarah Dettmer 3 Christin Helbig 3 Violaine Alunni 6 Marie-Annick Battaini 6 Carole Mura 6 Charlotte Henrichsen 7 Raquel Garcia-Lopez 8 Diego Echevarria 8 Eduardo Puelles 8 Elena Garcia-Calero 8 Stefan Kruse 9 Markus Uhr 3 Christine Kauck 3 Guangjie Feng 10 Nestor Milyaev 10 Chuang Kee Ong 10 Lalit Kumar 10 Meisze Lam 10 Colin Semple 10 Attila Gyenesei 10 Stefan Mundlos 2 Uwe Radelof 11 Hans Lehrach 2 Paolo Sarmientos 4 Alexandre Reymond 7 Duncan Davidson 10 Pascal Dollé 12, * Stylianos Antonarakis 5 Marie-Laure Yaspo 2 Salvador Martinez 8 Richard Baldock 10 Gregor Eichele 3 Andrea Ballabio 1, 13, 14, 15, *
Abstract : Ascertaining when and where genes are expressed is of crucial importance to understanding or predicting the physiological role of genes and proteins and how they interact to form the complex networks that underlie organ development and function. It is, therefore, crucial to determine on a genome-wide level, the spatio-temporal gene expression profiles at cellular resolution. This information is provided by colorimetric RNA in situ hybridization that can elucidate expression of genes in their native context and does so at cellular resolution. We generated what is to our knowledge the first genome-wide transcriptome atlas by RNA in situ hybridization of an entire mammalian organism, the developing mouse at embryonic day 14.5. This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org), consists of a searchable database of annotated images that can be interactively viewed. We generated anatomy-based expression profiles for over 18,000 coding genes and over 400 microRNAs. We identified 1,002 tissue-specific genes that are a source of novel tissue-specific markers for 37 different anatomical structures. The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organization for the hypothalamus, and insight on the Wnt network involved in renal epithelial differentiation during kidney development. The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease.
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Graciana Diez-Roux, Sandro Banfi, Marc Sultan, Lars Geffers, Santosh Anand, et al.. A high-resolution anatomical atlas of the transcriptome in the mouse embryo.. PLoS Biology, Public Library of Science, 2011, 9 (1), pp.e1000582. ⟨10.1371/journal.pbio.1000582⟩. ⟨inserm-00707211⟩

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