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Transposons in Embryo Space – TRACER maps in EMAGE

Posted by , on 9 February 2017

A recent publication in Developmental Biology by (Armit et al., 2017) describes how the TRACER dataset can be spatially compared with in situ hybridisation gene expression profiles.

An EMAGE entry with the accompanying spatial map of a TRACER regulatory element reporter in the E11.5 mouse embryo. The original data images are shown in the upper panel. The lower panel shows spatial annotation as a colour-map, with strong expression shown in red, and moderate expression shown in yellow. Cyan denotes regions of the embryo where expression is not detected. The spatially mapped pattern can be used to query the EMAGE database of 30K gene expression patterns.


  • The TRACER dataset of transposon-associated regulatory sensors (Chen et al., 2013) utilises Sleeping Beauty lacZ transposons that have been randomly integrated into the mouse genome
  • Hundreds of insertions have been mapped to specific genomic positions, and the corresponding regulatory potential is documented through lacZ imaging of E11.5 wholemount mouse embryos
  • Through spatial mapping of the lacZ expression patterns, the EMAGE gene expression database enables co-localisation and co-expression of regulatory elements to be explored computationally
  • Spatial mapping additionally enables rapid identification of cis-regulatory elements that are expressed in a region of interest in the mouse embryo


Click here to access the spatially mapped TRACER dataset in EMAGE.



Armit C, Richardson L, Venkataraman S, Graham L, Burton N, Hill B, Yang Y, Baldock RA. eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis, Developmental Biology, Available online 2 February 2017, ISSN 0012-1606,


Chen, C-K, Symmons O, Uslu VV, Tsujimura T, Ruf S, Smedley D, Spitz F. TRACER: a resource to study the regulatory architecture of the mouse genome. BMC Genomics 14 (2013), p. 215,

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