Bushra profiled over 200,000 cells from zebrafish brains during 12 developmental timepoints, spanning 12 hours to 15 days post-fertilization. Through clustering and annotation, she generated an incredibly comprehensive atlas of zebrafish brain development. Bushra and Jeff worked together to profile transcriptional trajectories and the gene expression cascades during the development of the retina and hypothalamus. Examination of the major gene expression programs in progenitor cells revealed that embryonic neural progenitors are primarily defined by spatial gene expression signatures, but that signature becomes dampened in long-term progenitors. The trajectories highlighted an interesting difference between fish and mammalian retinal development: namely that fish Muller glia cells seem to become transcriptionally distinct much earlier in development than mammalian ones. Additionally, our pseudotime analysis revealed different progenitor strategies between these two tissues. In the retina, late-stage progenitor cells transcriptionally resemble those from earlier embryonic development, while hypothalamic progenitors change over developmental time, and later-stage hypothalamic progenitors do not transcriptionally resemble those of the embryo.

Check it out in biorxiv!