A high-resolution anatomical atlas of the transcriptome in the mouse embryo.
IF: 9.593
Cited by: 500


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.


Temporal Gene Expression
Temporal Anatomic

MeSH terms

Atlases as Topic
Databases, Genetic
Embryo, Mammalian
Gene Expression Profiling
Mice, Inbred C57BL
Organ Specificity


Diez-Roux, Graciana
Banfi, Sandro
Sultan, Marc
Geffers, Lars
Anand, Santosh
Rozado, David
Magen, Alon
Canidio, Elena
Pagani, Massimiliano
Peluso, Ivana
Lin-Marq, Nathalie
Koch, Muriel
Bilio, Marchesa
Cantiello, Immacolata
Verde, Roberta
De Masi, Cristian
Bianchi, Salvatore A
Cicchini, Juliette
Perroud, Elodie
Mehmeti, Shprese
Dagand, Emilie
Schrinner, Sabine
Nürnberger, Asja
Schmidt, Katja
Metz, Katja
Zwingmann, Christina
Brieske, Norbert
Springer, Cindy
Hernandez, Ana Martinez
Herzog, Sarah
Grabbe, Frauke
Sieverding, Cornelia
Fischer, Barbara
Schrader, Kathrin
Brockmeyer, Maren
Dettmer, Sarah
Helbig, Christin
Alunni, Violaine
Battaini, Marie-Annick
Mura, Carole
Henrichsen, Charlotte N
Garcia-Lopez, Raquel
Echevarria, Diego
Puelles, Eduardo
Garcia-Calero, Elena
Kruse, Stefan
Uhr, Markus
Kauck, Christine
Feng, Guangjie
Milyaev, Nestor
Ong, Chuang Kee
Kumar, Lalit
Lam, MeiSze
Semple, Colin A
Gyenesei, Attila
Mundlos, Stefan
Radelof, Uwe
Lehrach, Hans
Sarmientos, Paolo
Reymond, Alexandre
Davidson, Duncan R
Dollé, Pascal
Antonarakis, Stylianos E
Yaspo, Marie-Laure
Martinez, Salvador
Baldock, Richard A
Eichele, Gregor
Ballabio, Andrea

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