Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
University of Basel · Allen Institute · +4 more institutions
Abstract
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…
Citation impact
- FWCI
- 65.84
- Percentile
- 100%
- References
- 93
Authors
19Topics & keywords
- Gastrulation
- Organogenesis
- Gene expression
- Transcriptome
- In situ hybridization
- Zebrafish
- Gene
- Regulation of gene expression