TY - JOUR T1 - A 3D molecular atlas of the chick embryonic heart JF - bioRxiv DO - 10.1101/609032 SP - 609032 AU - Claire Anderson AU - Bill Hill AU - Hui-Chun Lu AU - Adam Moverley AU - Youwen Yang AU - Nidia M.M. Oliveira AU - Richard A. Baldock AU - Claudio D. Stern Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/04/16/609032.abstract N2 - We present a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 micro-dissected regions reveals regionalised expression of 15,570 genes. Of these, 132 were studied by in situ hybridisation and a subset (38 genes) was mapped by Optical Projection Tomography or serial sectioning to build a detailed 3-dimensional atlas of expression. We display this with a novel interactive 3-D viewer and as stacks of sections, revealing the boundaries of expression domains and regions of overlap. Analysis of the expression domains also defines some sub-regions distinct from those normally recognised by anatomical criteria at this stage of development, such as a previously undescribed subdivision of the atria into two orthogonal sets of domains (dorsoventral and left-right). We also include a detailed comparison of expression in the chick with the mouse and other species. ER -