Knowing the ‘normal’ expression of genes during embryo development is key to understanding the differences that occur due to genetic mutations.

As part of work to understand the underlying transcriptional processes in developing embryos from knockout mouse lines, DMDD has now released a gene expression profile for wild-type mouse embryos between E8.5 and E10.5. The new dataset reveals the typical expression profile of genes during this crucial period of embryonic development, including their abundance, and when they are turned on and off.


RNA-seq has been used to establish the expression profile for whole, wild-type embryos at each somite number between 4 and 36 (excluding 29 – 33). This range corresponds roughly to the period E8.5 – E10.5, a vital period during which many organs and systems begin to develop.

The resulting data is now available in Expression Atlas. It’s a temporal baseline expression reference derived from wild-type embryos, which adds to EBI’s established resource to give a more complete picture of gene expression during embryonic development.


The wild-type baseline helps us to answer the question “what does ‘normal’ whole-embryo gene expression look like during development?” This is hugely important, as we can only really begin to explore what is abnormal once we know what is normal.

More specifically, the baseline highlights patterns in the way different genes are usually expressed as an embryo develops: when they are turned on and off; their abundance and whether their expression is covariant with other genes. Example expression profiles are shown below for Nacad and Pdzk1, indicating that at this depth of sequencing Nacad is switched on during somitogenesis and Pdzk1 is switched off.

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Expression profiles of the Nacad and Pdzk1 genes with increasing somite number. The white boxes indicate no expression at a cut off of 0.6 fpkm (fragments per kilobase per million). The numbers in the boxes give the level of expression in fpkm, with bluer boxes indicating a higher level of expression.


For DMDD, the new dataset will underpin work on molecular phenotyping, by allowing us to understand whether the expression patterns of mutant embryos are significantly different from the wild-type. The ultimate goal is to allow users to correlate a given gene with the physical manifestations of its knockout in the developing embryo, and the underlying transcriptional processes.

The relationship between gene, morphological phenotype and molecular phenotype in the DMDD programme.
The DMDD database will ultimately allow correlation between genes, morphological phenotypes and molecular phenotypes (based on transcriptional processes).

However the data is a valuable resource for any researcher interested in gene expression during embryonic development, and is free to use. You can explore the data further in Expression Atlas.