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Zachary V. Johnson, Email: zvjohns@emory.edu
These authors contributed equally: Zachary V. Johnson, Brianna E. Hegarty, George W. Gruenhagen.
We thank our collaborators Ashley Parker and Drs. Swantje Graetsch, Manuel Stemmer, and Herwig Baier for valuable feedback during the early stages of the project; Dr. Nicholas Johnson for suggestions regarding statistical analysis of IEG co-expression; Dr. Justin Rhodes for insightful feedback on IEG expression analysis; Dr. Cori Bargmann for thoughtful feedback on early drafts of the manuscript; Cristina Baker for her critical role in the initial development of spatial transcriptomics wetlab pipelines; and the Georgia Tech Petit Institute Genome Analysis and Molecular Evolution Cores for their integral roles in sample processing and sequencing, respectively.
General: Z.V.J. initially conceived of the experiment and Z.V.J., J.T.S., and B.E.H. developed and designed it. Z.V.J. and B.E.H. performed all wetlab work (see details below under “Wetlab”). T.J.L. pre-processed behavioral and depth data, including in part spatial and temporal registration of both data streams and temporal anchoring to experimental endpoints. G.W.G. pre-processed snRNA-seq, DNA-seq, and spatial transcriptomics data. Z.V.J. and G.W.G. performed downstream data analysis (see details below under “Drylab”). B.E.H. matched snRNA-seq data to published neuroanatomical expression profiles (see details below under “Drylab”). Z.V.J. took the lead on writing the manuscript with critical feedback from G.W.G., J.T.S., B.E.H., and P.T.M. Z.V.J. took the lead on designing and creating figures with contributions from B.E.H., G.W.G., and T.J.L., and with critical feedback from G.W.G., J.T.S., B.E.H., P.T.M., and T.J.L. J.T.S. mentored and funded Z.V.J., B.E.H., and G.W.G., and P.T.M mentored and funded T.J.L. on the project. J.T.S. funded snRNA-seq, DNA-seq, and spatial transcriptomics experiments. Wetlab: Z.V.J. and B.E.H. developed and optimized a single nucleus isolation protocol for cichlid telencephala. Z.V.J. and B.E.H. performed all behavioral assays, surgeries, and downstream nuclei isolations for snRNA-seq. Z.V.J. performed DNA isolations for matching nuclei to subjects. B.E.H. performed all behavior assays for spatial transcriptomics. Z.V.J. and B.E.H. performed surgeries for spatial transcriptomics. B.E.H. performed all downstream wetlab work for spatial transcriptomics. The Petit Institute Genome Analysis Core at GT performed library preparation for snRNA-seq, DNA-seq, and spatial transcriptomics. The Petit Institute Molecular Evolution Core at GT performed sequencing for snRNA-seq, DNA-seq, and spatial transcriptomics. Drylab: Z.V.J. performed clustering and cluster marker analysis. B.E.H. systematically surveyed the literature to determine conserved neuroanatomical expression patterns of ligand, receptor, nTF, and other cell type-specific marker genes in the teleost telencephalon. B.E.H., G.W.G., and Z.V.J. collaboratively identified markers of radial glial quiescence, cycling, and neuronal differentiation. Z.V.J. and G.W.G. collaboratively developed many analytical approaches. Z.V.J. conducted behavioral, IEG co-expression, IEG, DEG, pNG, cell proportion, and gene set enrichment (for biological categories) analyses. G.W.G. matched nuclei to subjects and conducted comparative genomics, gene orthologue calling, ERE detection, gene module detection, and cluster enrichment (for gene lists) analyses. G.W.G. performed spatial integration of clusters and B.E.H. matched spatial transcriptomic profiles to brain regions. Z.V.J. and G.W.G. performed cell–cell communication analyses.
The authors declare no competing interests.
This work was supported in part by NIH R01GM101095 and R01GM144560 to J.T.S., NIH F32GM128346 to Z.V.J., NIH R35 GM139594 to P.T.M., NSF Graduate Research Fellowship DGE-2039655 to T.J.L., and Human Frontiers Science Program RGP0052/2019 to J.T.S.
© The Author(s) 2023