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Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nürnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dollé P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 2011; 9:e1000582. [PMID: 21267068 PMCID: PMC3022534 DOI: 10.1371/journal.pbio.1000582] [Citation(s) in RCA: 467] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 12/06/2010] [Indexed: 11/23/2022] Open
Abstract
The manuscript describes the “digital transcriptome atlas” of the developing mouse embryo, 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. 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. In situ hybridization (ISH) can be used to visualize gene expression in cells and tissues in their native context. High-throughput ISH using nonradioactive RNA probes allowed the Eurexpress consortium to generate a comprehensive, interactive, and freely accessible digital gene expression atlas, the Eurexpress transcriptome atlas (http://www.eurexpress.org), of the E14.5 mouse embryo. Expression data for over 15,000 genes were annotated for hundreds of anatomical structures, thus allowing us to systematically identify tissue-specific and tissue-overlapping gene networks. We illustrate the value of the Eurexpress atlas by finding novel regional subdivisions in the developing brain. We also use the transcriptome atlas to allocate specific components of the complex Wnt signaling pathway to kidney development, and we identify regionally expressed genes in liver that may be markers of hematopoietic stem cell differentiation.
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Affiliation(s)
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | - Marc Sultan
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Geffers
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Santosh Anand
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | - David Rozado
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alon Magen
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Ivana Peluso
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | - Nathalie Lin-Marq
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Muriel Koch
- Institut Clinique de la Souris, Illkirch, France
| | - Marchesa Bilio
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | | | - Roberta Verde
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | | | | | - Juliette Cicchini
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Elodie Perroud
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Shprese Mehmeti
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emilie Dagand
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Asja Nürnberger
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Katja Schmidt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Katja Metz
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Norbert Brieske
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Cindy Springer
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ana Martinez Hernandez
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Sarah Herzog
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Frauke Grabbe
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Cornelia Sieverding
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Barbara Fischer
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Kathrin Schrader
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Maren Brockmeyer
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Sarah Dettmer
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Christin Helbig
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | | | | | - Carole Mura
- Institut Clinique de la Souris, Illkirch, France
| | | | - Raquel Garcia-Lopez
- Experimental Embryology Lab, Instituto de Neurociencias, Universidad Miguel Hernandez, San Juan de Alicante, Spain
| | - Diego Echevarria
- Experimental Embryology Lab, Instituto de Neurociencias, Universidad Miguel Hernandez, San Juan de Alicante, Spain
| | - Eduardo Puelles
- Experimental Embryology Lab, Instituto de Neurociencias, Universidad Miguel Hernandez, San Juan de Alicante, Spain
| | - Elena Garcia-Calero
- Experimental Embryology Lab, Instituto de Neurociencias, Universidad Miguel Hernandez, San Juan de Alicante, Spain
| | | | - Markus Uhr
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Christine Kauck
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
| | - Guangjie Feng
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Nestor Milyaev
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Chuang Kee Ong
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Lalit Kumar
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - MeiSze Lam
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Colin A. Semple
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Attila Gyenesei
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Uwe Radelof
- RZPD—Deutsches Ressourcenzentrum für Genomforschung, Berlin, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Duncan R. Davidson
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Pascal Dollé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Inserm U 964, CNRS UMR 7104, Faculté de Médecine, Université de Strasbourg; Illkirch, France
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- University Hospitals of Geneva, Geneva, Switzerland
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Marie-Laure Yaspo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Salvador Martinez
- Experimental Embryology Lab, Instituto de Neurociencias, Universidad Miguel Hernandez, San Juan de Alicante, Spain
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Richard A. Baldock
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Gregor Eichele
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Goettingen, Germany
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Medical Genetics, Department of Pediatrics, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, United States of America
- * E-mail: (DRD); (PD); (SEA); (M-LY); (SM); (RAB); (GE); (AB)
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