A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

Teleost fish form the largest group of vertebrates, making them critically important for the study on the mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon: the seat of plastic behavior, learning, and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using single-cell RNA-seq and spatial transcriptomics, resulting in de novo molecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conse..., , , This repository contains the data and code associated with the scientific article titled \"A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types\". The research employed various techniques, including single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics, to elucidate the molecular neuroanatomy and evolutionary aspects of the goldfish telencephalon. # Upload Files The following dataset files are available ### Dryad (Data) 1. **GF\_TE\_sc\_data\_2023.zip** \- Single\-cell datasets for the goldfish telencephalon used in the article\. This archive includes the following files: * `sc_data.csv` \- Single\-cell count matrix \(genes\- rows\, cells\- columns\)\. * `genes.csv` \- Genes list\. * `cell_type_name.csv` \- Cell type names list\. * `sample_region.csv` \- Table of flags indicating single cell \(rows\) with sample number\, region \(columns\)\. 2. **GF\_TE\_st\_data\_2023.zip** \- Spatial transcri...硬骨鱼（Teleost fish）是脊椎动物中最大的类群，因此在大脑演化机制的研究中具有至关重要的地位。事实上，硬骨鱼展现出与鸟类、哺乳类高度相似的多样适应性行为，但其介导此类行为的神经基础仍不甚明晰。我们针对金鱼端脑——脊椎动物可塑性行为、学习与记忆的核心脑区——开展了系统性的比较研究。通过单细胞RNA测序（single-cell RNA-seq）与空间转录组学技术，我们对金鱼端脑的细胞类型进行了注释与图谱绘制，构建了全新的分子神经解剖分区。在小鼠与金鱼分化的4.5亿年演化历程中，神经胶质细胞高度保守，而神经元的基因表达则呈现出多样性与模块化特征。具体而言，生长抑素（SST）中间神经元——这类在哺乳动物皮层中广泛分布以提供局部抑制性输入的细胞群，在金鱼端脑中却奇特地聚集于单个核团内，但在分子层面上……。 本仓库包含与题为《金鱼端脑细胞类型图谱揭示空间结构与细胞类型演化多样性》的学术论文相关的数据与代码。本研究采用单细胞RNA测序（scRNA-seq）与空间转录组学等多种技术，解析了金鱼端脑的分子神经解剖特征及其演化层面的相关问题。 # 上传文件 以下数据集文件可获取： ### Dryad（数据仓库） 1. **GF_TE_sc_data_2023.zip** — 本文中使用的金鱼端脑单细胞数据集。该压缩包包含以下文件： * `sc_data.csv` — 单细胞计数矩阵（行代表基因，列代表细胞）。 * `genes.csv` — 基因列表文件。 * `cell_type_name.csv` — 细胞类型名称列表文件。 * `sample_region.csv` — 标记单细胞（行）所属样本编号与脑区（列）的表格。 2. **GF_TE_st_data_2023.zip** — 空间转录组数据……