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

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

doi:10.1371/journal.pbio.1000582

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

Journal article

Open access

Peer reviewed

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

Graciana Diez-Roux, Sandro Banfi, Marc Sultan, Lars Geffers, Santosh Anand, David Rozado, Alon Magen, Elena Canidio, Massimiliano Pagani, Ivana Peluso, …

PLoS biology, Vol.9(1), pp.e1000582-e1000582

01/01/2011

DOI: https://doi.org/10.1371/journal.pbio.1000582

PMCID: PMC3022534

PMID: 21267068

Abstract

Animals

Atlases as Topic

Databases, Genetic

Development Biology

Embryo, Mammalian

Gene Expression Profiling

Internet

Life Sciences

Mice

Mice, Inbred C57BL

Organ Specificity

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 (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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Title: A high-resolution anatomical atlas of the transcriptome in the mouse embryo
Creators - without role: Graciana Diez-Roux - Telethon Institute Of Genetics And Medicine
Sandro Banfi - Telethon Institute Of Genetics And Medicine
Marc Sultan - Max Planck Institute for Molecular Genetics
Lars Geffers - Max Planck Institute for Biophysical Chemistry
Santosh Anand - Telethon Institute Of Genetics And Medicine
David Rozado - Max Planck Institute for Molecular Genetics
Alon Magen - Max Planck Institute for Molecular Genetics
Elena Canidio - Primm
Massimiliano Pagani - Primm
Ivana Peluso - Telethon Institute for Genetics and Medicine
Nathalie Lin-Marq - University of Geneva
Muriel Koch - Institut Clinique de la Souris
Marchesa Bilio - Telethon Institute Of Genetics And Medicine
Immacolata Cantiello - Telethon Institute Of Genetics And Medicine
Roberta Verde - Telethon Institute Of Genetics And Medicine
Cristian de Masi - Telethon Institute Of Genetics And Medicine
Salvatore Bianchi - Telethon Institute Of Genetics And Medicine
Juliette Cicchini - University of Geneva
Elodie Perroud - University of Geneva
Shprese Mehmeti - University of Geneva
Emilie Dagand - Max Planck Institute for Molecular Genetics
Sabine Schrinner - Max Planck Institute for Molecular Genetics
Asja Nürnberger - Max Planck Institute for Molecular Genetics
Katja Schmidt - Max Planck Institute for Molecular Genetics
Katja Metz - Max Planck Institute for Molecular Genetics
Christina Zwingmann - Max Planck Institute for Molecular Genetics
Norbert Brieske - Max Planck Institute for Molecular Genetics
Cindy Springer - Max Planck Institute for Molecular Genetics
Ana Martinez Hernandez - Max Planck Institute for Biophysical Chemistry
Sarah Herzog - Max Planck Institute for Biophysical Chemistry
Frauke Grabbe - Max Planck Institute for Biophysical Chemistry
Cornelia Sieverding - Max Planck Institute for Biophysical Chemistry
Barbara Fischer - Max Planck Institute for Biophysical Chemistry
Kathrin Schrader - Max Planck Institute for Biophysical Chemistry
Maren Brockmeyer - Max Planck Institute for Biophysical Chemistry
Sarah Dettmer - Max Planck Institute for Biophysical Chemistry
Christin Helbig - Max Planck Institute for Biophysical Chemistry
Violaine Alunni - Mouse Clinical Institute
Marie-Annick Battaini - Mouse Clinical Institute
Carole Mura - Mouse Clinical Institute
Charlotte Henrichsen - University of Lausanne
Raquel Garcia-Lopez - Universitat de Miguel Hernández d'Elx
Diego Echevarria - Universitat de Miguel Hernández d'Elx
Eduardo Puelles - Universitat de Miguel Hernández d'Elx
Elena Garcia-Calero - Universitat de Miguel Hernández d'Elx
Stefan Kruse - ORGARAT
Markus Uhr - Max Planck Institute for Biophysical Chemistry
Christine Kauck - Max Planck Institute for Biophysical Chemistry
Guangjie Feng - Western General Hospital
Nestor Milyaev - Western General Hospital
Chuang Kee Ong - Western General Hospital
Lalit Kumar - Western General Hospital
Meisze Lam - Western General Hospital
Colin Semple - Western General Hospital
Attila Gyenesei - Western General Hospital
Stefan Mundlos - Max Planck Institute for Molecular Genetics
Uwe Radelof - Deutsches Ressourcenzentrum für Genomforschung
Hans Lehrach - Max Planck Institute for Molecular Genetics
Paolo Sarmientos - Primm
Alexandre Reymond - University of Lausanne
Duncan Davidson - Western General Hospital
Pascal Dollé - University of Strasbourg
Stylianos Antonarakis - University of Geneva
Marie-Laure Yaspo - Max Planck Institute for Molecular Genetics
Salvador Martinez - Universitat de Miguel Hernández d'Elx
Richard Baldock - Western General Hospital
Gregor Eichele - Max Planck Institute for Biophysical Chemistry
Andrea Ballabio - Telethon Institute Of Genetics And Medicine
Publication Details: PLoS biology, Vol.9(1), pp.e1000582-e1000582
Publisher: Public Library of Science
Identifiers: 9943084908331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article