Data from: Cellular and transcriptional trajectories of neural fate specification in sea anemone uncover two modes of adult neurogenesis
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This archive contains raw data and code associated to the following publication: Cellular and transcriptional trajectories of neural fate specification in sea anemone uncover two modes of adult neurogenesis Plessier and Marlow, 2026, Nature Communications This archive is available for download here on zenodo Folders content: - _raw/: raw scRNA-Seq data matrix file used as the primary data source - _SeuratObjects/: processed and annotated Seurat objects (global KikGR+ cells clustering, each line-specific reclustering, progenitor-specific reclustering, and cnidocyte-specific reclustering) - _code/: contains the scripts for processing and analysis of scRNA-Seq data - _input/: contains input files required to run the scripts - _output/: output plots generated by the code Sequencing data availability: Raw sequencing reads for the scRNA-Seq dataset are available in the GEO repository GSE288441. These include paired-end fastq files for each of the 84 scRNA-Seq library in the paper, alongside the reference genome from the Darwin Tree of Life Consortium from the Wellcome Sanger Institute Tree of Life programme, NCBI GCF_932526225.1 RefSeq assembly and associated NCBI RefSeq gene models jaNemVect1.1 GTF with the KikGR transgene sequence added to both. These also include cell metadata information and raw and filtered global count tables. Softwares: R (4.4.1) open source packages Seurat (5.2.1), tidyverse (2.0.0), WGCNA (1.73), SeuratObject (5.0.2), reshape2 (1.4.4), ggnetwork (0.5.13), ggraph (2.2.1), ggnetwork (0.5.13), igraph (2.1.4), dynamicTreeCut(1.63-1), stringr (1.5.1), tidyr (1.3.1), dplyr (1.1.4), here (1.0.1), purr (1.0.4), ggplot2 (3.5.1), fgsea (1.30.0), patchwork (1.3.0), writexl (1.5.1). readxl (1.4.5), slingshot (2.12.0), viridis (0.6.5), viridisLite (0.4.2), mgcv(1.9-1), ggtext (0.1.2).
本存档包含与以下发表论文相关的原始数据与代码： 海葵神经命运特化的细胞与转录轨迹揭示两种成体神经发生模式 Plessier与Marlow，2026，《自然·通讯（Nature Communications）》 本存档可在Zenodo平台获取下载。 文件夹内容如下： - `_raw/`：作为核心数据源的原始单细胞RNA测序（single-cell RNA sequencing, scRNA-Seq）数据矩阵文件 - `_SeuratObjects/`：经过处理与注释的Seurat对象，包含全局KikGR阳性细胞聚类、各谱系特异性重聚类、祖细胞特异性重聚类以及刺细胞特异性重聚类结果 - `_code/`：用于scRNA-Seq数据处理与分析的脚本文件 - `_input/`：运行脚本所需的输入文件 - `_output/`：代码生成的可视化输出图表 测序数据获取说明：本scRNA-Seq数据集的原始测序读段可于基因表达汇编（Gene Expression Omnibus, GEO）数据库GSE288441中获取。其中包含论文中84个scRNA-Seq文库的双端fastq文件，以及来自威康桑格研究所生命之树项目的达尔文生命之树联盟参考基因组：NCBI GCF_932526225.1 RefSeq组装版本，还有添加了KikGR转基因序列的关联NCBI RefSeq基因模型jaNemVect1.1基因转移格式（Gene Transfer Format, GTF）文件。此外还包含细胞元数据信息，以及原始与过滤后的全局计数表格。 使用软件：R (4.4.1) 及以下开源工具包：Seurat (5.2.1)、tidyverse (2.0.0)、WGCNA (1.73)、SeuratObject (5.0.2)、reshape2 (1.4.4)、ggnetwork (0.5.13)、ggraph (2.2.1)、igraph (2.1.4)、dynamicTreeCut(1.63-1)、stringr (1.5.1)、tidyr (1.3.1)、dplyr (1.1.4)、here (1.0.1)、purr (1.0.4)、ggplot2 (3.5.1)、fgsea (1.30.0)、patchwork (1.3.0)、writexl (1.5.1)、readxl (1.4.5)、slingshot (2.12.0)、viridis (0.6.5)、viridisLite (0.4.2)、mgcv(1.9-1)、ggtext (0.1.2)
