Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Summary
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluorescent in situ hybridization (weMERFISH). We quantified the expression of 495 genes in zebrafish embryos at subcellular resolution and generated an online atlas detailing the expression of 25,872 genes and accessibility of 294,954 chromatin regions during embryogenesis. Expression patterns often
Content
# Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
*Published: 2026 Mar 12*
Gene expression patterns underlie development, but their systematic detection in
whole embryos has remained elusive. We introduce a whole-embryo imaging platform
using multiplexed error-robust fluorescent in situ hybridization (weMERFISH). We
quantified the expression of 495 genes in zebrafish embryos at subcellular
resolution and generated an online atlas detailing the expression of 25,872
genes and accessibility of 294,954 chromatin regions during embryogenesis.
Expression patterns often corresponded to composites of tissue-specific
accessible elements, and expression changes aligned with cellular maturation and
morphogenesis. Integration with live imaging revealed how similar expression
patterns can emerge through different dynamics and showed that sharp boundaries
develop through changes in gene expression rather than through cell sorting.
These results establish multiplexed whole-embryo spatial transcriptomics and
reveal the regulation and dynamics of embryonic gene expression patterns.
DOI: 10.1126/science.adt3439