A high-resolution anatomical atlas of the transcriptome in the mouse embryo.
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.
Telethon Institute of Genetics and Medicine, Naples, Italy.
Graciana
G
Diez-Roux
Sandro
S
Banfi
Marc
M
Sultan
Lars
L
Geffers
Santosh
S
Anand
David
D
Rozado
Alon
A
Magen
Elena
E
Canidio
Massimiliano
M
Pagani
Ivana
I
Peluso
Nathalie
N
Lin-Marq
Muriel
M
Koch
Marchesa
M
Bilio
Immacolata
I
Cantiello
Roberta
R
Verde
Cristian
C
De Masi
Salvatore A
SA
Bianchi
Juliette
J
Cicchini
Elodie
E
Perroud
Shprese
S
Mehmeti
Emilie
E
Dagand
Sabine
S
Schrinner
Asja
A
Nürnberger
Katja
K
Schmidt
Katja
K
Metz
Christina
C
Zwingmann
Norbert
N
Brieske
Cindy
C
Springer
Ana Martinez
AM
Hernandez
Sarah
S
Herzog
Frauke
F
Grabbe
Cornelia
C
Sieverding
Barbara
B
Fischer
Kathrin
K
Schrader
Maren
M
Brockmeyer
Sarah
S
Dettmer
Christin
C
Helbig
Violaine
V
Alunni
Marie-Annick
MA
Battaini
Carole
C
Mura
Charlotte N
CN
Henrichsen
Raquel
R
Garcia-Lopez
Diego
D
Echevarria
Eduardo
E
Puelles
Elena
E
Garcia-Calero
Stefan
S
Kruse
Markus
M
Uhr
Christine
C
Kauck
Guangjie
G
Feng
Nestor
N
Milyaev
Chuang Kee
CK
Ong
Lalit
L
Kumar
MeiSze
M
Lam
Colin A
CA
Semple
Attila
A
Gyenesei
Stefan
S
Mundlos
Uwe
U
Radelof
Hans
H
Lehrach
Paolo
P
Sarmientos
Alexandre
A
Reymond
Duncan R
DR
Davidson
Pascal
P
Dollé
Stylianos E
SE
Antonarakis
Marie-Laure
ML
Yaspo
Salvador
S
Martinez
Richard A
RA
Baldock
Gregor
G
Eichele
Andrea
A
Ballabio
D000818:Animals; D001271:Atlases as Topic; D030541:Databases, Genetic; D004622:Embryo, Mammalian; D020869:Gene Expression Profiling; D020407:Internet; D051379:Mice / Q000033:anatomy & histology* / Q000196:embryology / Q000235:genetics*; D008810:Mice, Inbred C57BL; D009928:Organ Specificity
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