Fig. 1: Reconstruction of gene expression patterns in the avian gastrula.
From: Spatial patterning of the epigenome during vertebrate gastrulation
a Spatial transcriptomic analysis was performed via cryosectioning 100 μm sections of late gastrula stage (HH5) embryos along the anteroposterior (AP) and mediolateral axes (ML). b Individual tissue sections were subsequently processed for 3’ RNA-seq. c Multiplexed HCR in situ hybridization showing the expression of OTX2, MEOX2, and TBXT in the HH5 chicken gastrula. Density plots to the right display normalized gene expression profiles along the AP axis derived from analysis of the tomo-seq datasets. Scale bar: 400 μm. d Integration of AP and ML transcriptomic datasets allows for quantification of gene expression in two dimensions across the avian gastrula. The two-dimensional expression of OTX2 is shown for reference (e). e In silico (left) reconstruction of the OTX2, CHRD, MEOX1, and TBXT 2D gene expression patterns, along with the corresponding in situ hybridization images (right). In silico projections recapitulate the gene expression profiles as seen via in situ hybridization. Scale bar: 400 μm. f Heatmap showing 706 anterior- and 294 posterior-enriched genes (p-value < 0.01, log fold change >1/ < −1) expressed in the avian gastrula, as determined via TradeSeq’s startVsEndTest function. g Spatial averages of anterior and posterior genes in the gastrula. Source data are provided as a Source Data file. AP anteroposterior, ML mediolateral.
