Diatom (Thalassiosira pseudonana) gene information from experiments designed to study single-cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms conducted in December of 2022

This dataset includes gene information for diatom Thalassiosira pseudonana grown during an experiment conducted as part of a study of \"Single-Cell transcriptional profiling of nutrient acquisition heterogeneity in diatoms.\" See \"Related Datasets\" section for T. pseudonana physiological data and cell information collected as part of the same study and experiments.

Study description:

Diatoms (Bacillariophyceae) are unicellular photosynthetic algae, accounting for about 40% of total marine primary production (equivalent to terrestrial rainforests) and critical ecological players in the contemporary ocean. Diatoms can form enormous blooms in the ocean that can be seen from space and are the base of food webs in coastal and upwelling systems, support essential fisheries, and are central to the biogeochemical cycling of important nutrients such as carbon and silicon. Over geological time, diatoms have influenced the world's climate by changing the carbon flux into the oceans.

Diatoms have traditionally been studied on a population level. Growth is often measured by the total increase in biomass, and gene expression is analyzed by isolating mRNA from thousands or millions of cells. These methods generate a valuable analysis on the population’s average functioning; however, they fail to show how each individual diatom cell contributes to the population phenotype. Bulk transcriptomes confound different stages and variability of cell states in heterogeneous populations. By contrast, single-cell transcriptomics measures gene expression in thousands of individual diatoms providing a quantitative and ultrahigh-resolution picture of transient cell states in population fractions enabling the reconstruction of the various phenotypic trajectories. Thus, the single-cell physiological and molecular parameters analysis allows an unsupervised assessment of cell heterogeneity within a population—a new dimension in diatoms and phytoplankton in general.

In this dataset, we examine the model diatom Thalassiosira pseudonana clonal cells grown in different nitrogen conditions, at the single cell level when grown in a light: dark cycle (12:12 h). Nitrogen is the major limiting nutrient for primary production and growth in the ocean’s surface, specifically for diatoms and the food webs they support. We investigate nutrient limitation, starvation and recovery. We used droplet-based, single-cell transcriptomics to analyze ten samples in two stages. In the first stage (\"starvation\"), six samples were collected over four days of culture as nutrient levels decreased. In the second stage (\"recovery\"), four samples were collected over twelve hours after nutrients were replenished.

本数据集包含参与"硅藻营养获取异质性的单细胞转录组分析"相关实验的假微型海链藻（Thalassiosira pseudonana）的基因信息。有关该研究与实验中采集的假微型海链藻生理数据及细胞信息，请参见"相关数据集"章节。

研究描述：
硅藻（Bacillariophyceae，硅藻门）是单细胞光合藻类，约占海洋总初级生产力的40%（等效于陆地热带雨林），是现代海洋中至关重要的生态参与者。硅藻可在海洋中形成肉眼乃至太空可见的大规模水华，作为沿岸与上升流系统食物网的基础支撑着重要渔业，同时在碳、硅等关键营养元素的生物地球化学循环中发挥核心作用。在地质时间尺度上，硅藻通过改变海洋碳通量对全球气候产生了深远影响。

传统硅藻研究多基于群体水平：通常以生物量总增量衡量生长状态，通过从数千乃至百万级细胞中分离mRNA开展基因表达分析。此类方法可获取群体平均功能的有效解析，但无法揭示单个硅藻细胞对群体表型的具体贡献。批量转录组（bulk transcriptome）会混淆异质性群体内细胞状态的不同阶段与变异情况。与之相对，单细胞转录组学可对数千个单个硅藻的基因表达进行检测，定量且以超高分辨率呈现群体组分中的瞬时细胞状态，进而实现各类表型轨迹的重构。因此，单细胞生理与分子参数分析可实现群体内细胞异质性的无监督评估——这为硅藻乃至整个浮游植物研究开辟了全新维度。

本数据集以模式硅藻假微型海链藻（Thalassiosira pseudonana）的克隆细胞为研究对象，实验设置了不同氮营养条件，在12:12小时的光暗周期下以单细胞水平开展分析。氮是海洋表层初级生产与生长的主要限制营养元素，对硅藻及其支撑的食物网尤为关键。本研究聚焦营养限制、饥饿及恢复过程，采用基于液滴的单细胞转录组技术，分两个阶段对10个样本进行分析：第一阶段为"饥饿期"，在培养4天内随营养水平逐步下降收集了6个样本；第二阶段为"恢复期"，在营养补充后的12小时内收集了4个样本。