We are beginning the process of deriving molecular phenotypes for our knockout lines. The first stage has been to understand gene expression in wild-type embryos, to produce a temporal baseline expression reference. The baseline highlights patterns in the way that different genes are normally expressed as an embryo develops: when they are switched on and off; their abundance and whether their expression is covariant with other genes.

This dataset provides a control against which mutant transcriptome data can be compared, in order to understand the effect of individual gene knockouts on whole-embryo gene expression.

Experimental technique

RNA-seq was used to establish the expression profiles for whole, wild-type mouse embryos of known sex 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 interpreted data is available in Expression Atlas as a temporal baseline expression reference.

Example expression profiles for the genes Nacad and Pdzk1. The data indicates that at this depth of sequencing Nacad is switched on during somitogenesis and Pdzk1 is switched off.