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Peer-reviewedCC BYScience

Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum

  • Kutay Deniz Atabay1
  • Patrick Aoude1
  • Chanyoung Park1
  • Mykola Kadobianskyi2
  • Olivier H. Paugois1
  • Benjamin Judkewitz2
  • Peter W. Reddien3,4,1
4 affiliations
  1. 1Whitehead Institute for Biomedical Research, Cambridge, MA, USA
  2. 2Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité–Universitätsmedizin Berlin, Berlin, Germany
  3. 3Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
  4. 4Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
Open at sourceDOICite

Abstract

A complete cell type transcriptome atlas of a vertebrate could promote understanding of animal cell type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleost Danionella cerebrum brings whole-vertebrate single-cell profiling experiments within reach. We performed region-stratified single-cell RNA sequencing across the adult Danionella body and mapped cell types and gene expression at single-cell resolution using spatial transcriptomics. We delineated spatially distinct neural cell types on the basis of their regional gene expression signatures. The body-wide atlas elucidated cell types harboring adult molecular positional memory, uncovered paedomorphic features, and revealed conserved body-region and appendage-specification programs in adult connective tissue. Comparative analyses revealed conserved neural cell types, and regeneration datasets uncovered expression dynamics during telencephalon regeneration. This whole-vertebrate transcriptome atlas yields a comprehensive resource for myriad questions in biology and neuroscience.

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Cite

BibTeXRIS
BibTeX
@article{atabay2026wholebody,
  title = {{Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum}},
  author = {Kutay Deniz Atabay and Patrick Aoude and Chanyoung Park and Mykola Kadobianskyi and Olivier H. Paugois and Benjamin Judkewitz and Peter W. Reddien},
  journal = {Science},
  year = {2026},
  month = oct,
  doi = {10.1126/science.aeg1125},
  url = {https://doi.org/10.1126/science.aeg1125},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Whole-body single-cell atlas of an adult vertebrate, Danionella cerebrum
AU  - Kutay Deniz Atabay
AU  - Patrick Aoude
AU  - Chanyoung Park
AU  - Mykola Kadobianskyi
AU  - Olivier H. Paugois
AU  - Benjamin Judkewitz
AU  - Peter W. Reddien
PY  - 2026
DA  - 2026/10/29
JO  - Science
DO  - 10.1126/science.aeg1125
UR  - https://doi.org/10.1126/science.aeg1125
AB  - A complete cell type transcriptome atlas of a vertebrate could promote understanding of animal cell type composition, organization, and evolution. The miniaturized, transparent, and regenerative teleost Danionella cerebrum brings whole-vertebrate single-cell profiling experiments within reach. We performed region-stratified single-cell RNA sequencing across the adult Danionella body and mapped cell types and gene expression at single-cell resolution using spatial transcriptomics. We delineated spatially distinct neural cell types on the basis of their regional gene expression signatures. The body-wide atlas elucidated cell types harboring adult molecular positional memory, uncovered paedomorphic features, and revealed conserved body-region and appendage-specification programs in adult connective tissue. Comparative analyses revealed conserved neural cell types, and regeneration datasets uncovered expression dynamics during telencephalon regeneration. This whole-vertebrate transcriptome atlas yields a comprehensive resource for myriad questions in biology and neuroscience.
SN  - 0036-8075
SN  - 0193-4511
SN  - 1095-9203
ER  -