The name of this database, "EMBRYS", is an acronym standing for Embryonic gene expression Database as a Biomedical Research Source. The construction of EMBRYS represents one of the approaches for biomedical sciences in the Post-Genomic Era, in which more functional information beyond mare DNA sequences is assembled in a more comprehensive as well as systematic fashion. We believe that EMBRYS serves as an essential source for the research in developmental biology.
Moreover, "EMBRYS" was coined by the combination of two words: EMBRYO + EBISU. Ebisu is known as one of the seven gods of good fortune in a Japanese myth, who was born without arms and legs and struggled to survive due to this hardship. However, he grew the skeletal structures at the age of three, overcame his birth defects, and became the god.
Thus, in this context, we wish that the information obtained from EMBRYS ultimately turns out to be an initial step toward the understanding of the mechanisms of congenital anomalies and the development of effective remedies. The major features of EMBRYS are as follows:
EMBRYS contains the data of gene expression patterns mapped in the whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which the most striking dynamics in pattern formation and organogenesis is observed. If the expression of a given gene was found interesting, embryos at other stages were also assayed to profile more detailed expression patterns.
Our primary interest is the gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. To obtain a comprehensive list for assays, the genes were extracted from the public databases including RIKEN Transcription Factor Database (http://genome.gsc.riken.jp/TFdb/) and Panther Classification System (http://www.pantherdb.org/). Consequently, we listed 2,911 genes, which comprise one of the most comprehensive list of TFs and TF-related factors around the globe at present. A large portion of the cDNA clones of these genes were obtained from RIKEN (Yokohama, Japan), and the rest was compensated by the MGC cDNA library, which is commercially available, or were otherwise generated at SBM. To date, 1,670 clones have been available for probe synthesis, out of which1,561 genes have been assayed, producing 24,545 photographs in addition to the annotation of gene expression.
3.Annotation of Gene Expression Patterns
One of the excellent aspects of EMBRYS is that the gene expression is annotated according to the anatomical structures and signal intensity. The localization of the gene expression is evaluated by taking advantage of the whole-mount assays: the regions evaluated range over multiple tissues and organs including brain, craniofacial region, limb, heart, liver, somite, tail and neural tube. The signal intensity is also evaluated as: (1) intense signal, (2) faint signal, (3) no signal, or not determined due to the obscure staining.[See more...]
We have adopted a rotational imaging system, which allows for three-dimensional recording of the entire embryo by streaming serial 2D images. By using the rotary head attached to the CCD camera, the image is captured at 2-degree intervals. This translates into 180 images taken for each embryo, which which together produce a motion picture by sequentially shown in an automatic manner. Thus, the embryo can be observed from any lateral angle you desire as if you were manipulating it at hand. [See more about AERO] or [See the Quick Guide]
- Species: Mouse (Mus Musculus)
- Strain: ICR
- Developmental Stages: E9.5, 10.5, 11.5 (other stages are included for several genes)
- Genes assayed: 1,561 Transcription factors and other related genes that are potentially involved in transcriptional activity
- # of 2D Images: E9.5- 7,219 E10.5- 7,958 E11.5- 8,536 Other stages- 558 Total- 24,171
- # of AERO Images: E9.5- 274 E10.5- 281 E11.5- 306 Total- 861
- Annotation of gene expression: Limb bud, Somite, Tail bud, Heart, Liver, Jaw, Eye, External genitalia, Olfactory placode, Spinal cord