Dataset Information

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

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.

SUBMITTER: Diez-Roux G

PROVIDER: S-EPMC3022534 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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

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

PLoS biology 20110118 1

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 nat ...[more]

PMID: 21267068

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Project description:The elderly males undergo degenerative fertility and testicular endocrine function that jeopardize the reproductive health and well-being. However, the mechanisms underlying reproductive aging are unclear. Here, we tried to address this by investigating the phenotypes and transcriptomes of seven regions of the male mouse reproductive tract: the testis, efferent ductules, initial segment, caput, corpus and cauda epididymidis, and vas deferens, in adult (3 months) and aged (21 months) mice. Quantitative PCR, immunohistochemistry, immunofluorescent staining, and enzyme-linked immunosorbent assay were performed for the analysis of gene expression in mice, human tissues, and semen samples. Aged male mice showed both systematic and reproductive changes, and remarkable histological changes were detected in the testis and proximal epididymis. Transcriptomes of the male reproductive tract were mapped, and a series of region-specific genes were identified and validated in mouse and/or human tissues, including Protamine 1 (Prm2), ADAM metallopeptidase domain 28 (Adam28), Ribonuclease A family member 13 (Rnase13), WAP four-disulfide core domain 13 (Wfdc13), and Wfdc9. Meanwhile, age-related transcriptome changes of different regions of the male reproductive tract were characterized. Notably, increased immune response was functionally related to the male reproductive aging, especially the T cell activation. An immune response-associated factor, phospholipase A2 group IID (Pla2g2d), was identified as a potential biomarker for reproductive aging in mice. And the PLA2G2D level in human seminal plasma surged at approximately 35 years of age. Furthermore, we highlighted Protein tyrosine phosphatase receptor type C (Ptprc), Lymphocyte protein tyrosine kinase (Lck), Microtubule associated protein tau (Mapt), and Interferon induced protein with tetratricopeptide repeats 3 (Ifit3) as critical molecules in the aging of initial segment, caput, caput, and cauda epididymidis, respectively. This study provides an RNA-seq resource for the male reproductive system during aging in mice, and is expected to improve our understanding of male reproductive aging and infertility.

Dataset Information

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

Publications

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

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